Abstract:
The present invention relates to rRNA-derived cDNA used as an internal standard or control to achieve normalization of hybridization signal detection in microarray biochip technology. Analysis of data obtained from a laser scanner during DNA microarray experiments first requires image processing. However, the data generated for the arrayed genes must be normalized before differentially expressed genes can be identified. Normalization is necessary to compensate for differences in labelling and detection efficiencies for the labels and for differences in the quantity of starting RNA from the samples examined in the assay. Because of its relatively invariant expression across tissues and treatments, 18S and 28S ribosomal RNAs are ideal internal controls for quantitative RNA analysis. A way to circumvent the technical difficulties of using ribosomal RNA as a control, because of its overabundance relative to that of other RNAs, is described and claimed in the present application. Improved methods, arrays, and kits comprising arrays and free unlabelled ribosomal probes, are objects of this invention. The unlabelled ribosomal probes are used to compete out the excess or ribosomal nucleics present in a sample wherein all cDNA species of the sample are labelled before being placed in contact with the arrays.

Description:
FIELD OF THE INVENTION  
         [0001]    The present invention relates to the field of hybridization arrays. More specifically, the present invention concerns a method for normalizing signals to be compared in hybridization arrays. This novel method relies on the use of ribosomal RNA (rRNA) as an internal standard and allows approximation of the relative abundance of multiple mRNAs as well as direct comparisons between any two specific RNA samples.  
         BACKGROUND OF THE INVENTION  
         [0002]    In DNA microarray experiments, one of the more popular ways to control for spotted DNA quantity and surface chemistry anomalies involves the use of two-color fluorescence (see, refs. 4, 5). For example, a Cy3 (green)-labelled probe prepared from healthy tissue could be used as a control to examine expression profiles of a Cy5 (red)-labelled probe prepared from a tumor tissue. The normalized expression values for every gene would then be calculated as the ratio of experimental expression to control expression. This method can obviously eliminate much (but not all) experimental variation by allowing two samples to be compared on the same chip because there is enough DNA on each spot that both test and reference cDNAs can hybridize to it at once without interference. More sophisticated three-color experiments are also possible in which one channel serves as a control for the amount of spotted DNA, and channels two and three allow two samples to be compared to this control and to each other (see ref. 5).  
           [0003]    In addition to the local normalization method described above, more general methods are also available in the form of control spots on the slide. With a set of control spots, it is possible to control variations in overall slide quality or scanning differences.  
           [0004]    Applicable normalization strategies are based on some underlying assumptions regarding the data and the strategies used for each experiment. These strategies must therefore be adjusted to reflect both the system under study and the experimental design. A primary assumption is that for either an entire collection of arrayed genes or some subset of the genes (such as housekeeping genes), or for some added set of controls, the ratio of measured expression averaged over the set should be close to unity.  
           [0005]    The need for good methods of normalisation for microarray data can not be overstated (see refs. 6, 7). Depending on the experimental design, there are three useful approaches for calculating normalization factors. The first simply relies on the total fluorescent intensity measured. The assumption underlying this approach is that the total mass of RNA labelled with either Cy3 or Cy5 is equal. While the intensity for any one spot may be higher in one channel than the other, when averaged over thousands of spots in a given array, these fluctuations average out. Consequently, the total integrated intensity across all the spots in the array should be equal for both channels. Alternatively, one could add a number of controls in increasing but equimolar concentrations to both labeling reactions, and the sum of the intensities for these spots should be equal.  
           [0006]    A second approach uses linear regression analysis. For closely related samples, one would expect many of the genes to be expressed at nearly constant levels. Consequently, a scatter plot of the measured Cy5 versus Cy3 intensities should have a slope of one. Measured intensities for added equimolar controls should behave similarly. Under this assumption, one can use regression analysis techniques to calculate the slope which is used to rescale the data and adjust the slope to one.  
           [0007]    A third approach has been described by Chen et al (1997) (ref. 1). In it, it is assumed that a subset of housekeeping genes exists and that for these genes the distribution of transcription levels should have some mean value and standard deviation that are independent of any particular sample. In this case, the ratio of measured Cy5 to Cy3 ratios for these genes can be modeled and the mean of the ratio adjusted to 1. Chen and his collaborators describe an iterative procedure to achieve this normalization. Quackenbush and collaborators (ref. 2) have implemented their own algorithm and a variation thereof that uses the entire data set in a data visualization and analysis tool called TIGR ArrayViewer. Other statistical methods of determining data accuracy have been described (ref. 3, 11).  
           [0008]    The above procedures describe array-based measures that can be used to normalize data. However, even with multiple colour fluorescence and control spots, undesired experimental variation can contaminate expression data. It is also possible that some or all of the physical normalization techniques are missing from the experiment, in which case it is even more important to find additional means of normalization.  
           [0009]    The use of internal standards overcomes these problems. Using an exogenously added standard has the advantage of giving the user absolute control over the amount of template added, with no variation between samples. Using an exogenous standard does not, however, control differences in the quality of the starting RNA in a reverse transcription reaction. If there are differences in the levels of integrity of the RNA between otherwise identical samples, the yield of specific reverse transcriptase products will reflect this variation, although the external standards will still appear identical. For this reason, as well as for simplicity and reproducibility, an endogenous RNA standard should be favoured in microarray experiments.  
           [0010]    Theoretically, an ideal endogenous standard for a DNA microarray would be a transcript whose expression does not vary during the cell cycle, between cell types, or in response to the experimental treatments that one wishes to examine. Additionally, for an endogenous standard to be valid in a microarray it is crucial that it be of a similar relative abundance as the test and reference (or target) transcripts in the microarray. Unfortunately, such a molecule does not exist and there are serious limitations to the standards currently in use. For example, although beta-actin is a frequently used standard (refs 9, 10), its level of expression varies significantly from tissue to tissue.  
           [0011]    For DNA microarray experiments, mRNA is copied into cDNA with the use of reverse transcriptase so that the relative abundance of individual mRNAs is reflected in the cDNA product. Input RNA in reverse transcription reactions is usually quantified by spectrophotometry. The RNA that is used in a typical pre-reverse transcription reaction is total RNA, 80% of which is ribosomal RNA. The mRNA component of total cellular RNA can vary from 2% to 5% depending on the tissue, the remainder of the RNA consisting of tRNA or small nuclear RNAs. Therefore, even if a transcript is invariant (as expressed as a percentage of mRNA), its relative abundance would still vary when considered as a percent of the total input RNA from different source tissues. Since the majority of the RNA is rRNA, the level of rRNA remains essentially constant from sample to sample. Because 18S and 28S rRNA make up the majority of optically absorbent material at OD 260nm , they should make ideal invariant controls. In fact, 18S and 28S transcripts are frequently used as internal controls in northern hybridization, RNAse protection and quantitative RT-PCR assays (see ref. 8). However, the overwhelming abundance of rRNA is a major limitation to its utility as a control in DNA microarray experiments.  
           [0012]    In U.S. Pat. No. 6,057,134, Ambion describes a method to perform RT-PCR™ which allows an invariant transcript of any relative abundance such as an 18S, 28S, or 5S ribosomal RNA, actin, or glyceraldehyde 3-P phosphate dehydrogenase RNA to be used as a control for any other transcript. This allows two targets of vastly different abundance to be quantified simultaneously in a multiplex RT-PCR™ reaction. Ambion uses blocked primers, or Competimers™, that compete with the unmodified primers for binding to a DNA template but cannot be used as primers for extension by a DNA polymerase Thus, at each extension step in PCR™, a percentage of template is unavailable for amplification. By increasing the ratio of Competimers™ to primers in a PCR™ reaction, the amplification efficiency of an amplicon can be reduced so that the linear phase of accumulation of PCR™ product matches that of a less abundant target in multiplex PCR™.  
           [0013]    For a control to be usable for microarray hybridization, the intensity of the signal should be in the same dynamic range as the cDNA under evaluation. rRNA-derived cDNA has never previously proved useful as a control for microarrays probably because it is thousands of times too abundant compared to specific cDNA.  
         OBJECTS OF THE INVENTION  
         [0014]    An object of the present invention is therefore to provide an improved method for providing an internal standard for normalizing the relative intensities of signals in hybridization arrays, an improved method for normalizing per se and a method of hybridizing making use of the improved normalization.  
         SUMMARY OF THE INVENTION  
         [0015]    More specifically, in accordance with the present invention, there is provided an improved method for providing an internal standard for normalizing the relative intensities of signals in hybridization arrays that is based on the use of ribosomal RNA (rRNA) as this internal standard. Ribosomal RNA has been found to be particularly suitable for this purpose because its abundance, in terms of percentage of total RNA, does not vary through the cell cycle or with a particular treatment.  
           [0016]    The method of the present invention may be summarized as follows. On a given DNA microarray, for example, an oligonucleotide specifically recognizing a sequence contained in ribosomal RNA is spotted along with the other DNA probes used to analyze gene expression, as is usual with this technique. The spots therefore essentially consist of capture probes. Ribosomal RNA, being of relatively invariant quantity in terms of percentage relative to total RNA provides a stable quantitative control to evaluate the quantity of other types of RNA. However, since it is also found in massive amounts relative to other RNAs, its level of detection by the technique must be toned down while remaining accurate. To that end, an experimentally-defined quantity of oligonucleotides carrying the same sequence as that of the oligonucleotide capture probe found on a spot of the microarray is added to the hybridization mixture so that the excess signal coming from the labelled rRNA (or from the cDNA generated from the rRNA, if cDNA hybridization is the method selected) is competed out and the signal detected for it is reduced to a range compatible with that of the signal for the other labelled RNAs.  
           [0017]    Specifically, the present invention provides a novel method for providing an internal standard for normalizing the relative intensities of signals on a hybridization array, comprising:  
           [0018]    adding a known quantity of an unlabelled ribosomal nucleic acid competitor probe into a hybridization buffer suitable for the array experiment, the competitor probe characterized in that it has the same sequence as at least portion of a capture probe present in the array for immobilizing ribosomal nucleic acids thereon; and  
           [0019]    allowing the competitor probe to compete with a ribosomal capture probe for hybridization to a suitably labelled RRNA-derived cDNA of a cDNA sample, such that a hybridization signal of labelled rRNA-derived cDNA is decreased to a suitable signal dynamic range of detection and the rRNA-derived cDNA of the sample becomes a suitable internal standard for the hybridization array.  
           [0020]    The method of the present invention may further include:  
           [0021]    determinating the quantity of hybridized rRNA-derived cDNA; and  
           [0022]    comparing the quantity of hybridized rRNA-derived cDNA against standard curves to determine the quantity of cDNA in said sample.  
           [0023]    The present invention further provides a normalization method, wherein the above steps for obtaining an internal standard are reproduced for a test sample using a first label, and for a suitably-labelled reference sample using a second label, and the quantity of hybridized rRNA-derived cDNA originating from the test sample is compared to the quantity of rRNA-derived cDNA originating from the reference sample hybridizing to the same capture probe to provide a normalization factor.  
           [0024]    The present invention further provides a hybridization array, wherein the above steps for normalizing are reiterated and the normalization factor is used to correct a hybridization signal provided by the binding of a target cDNA of the test sample labelled with the first label to a capture probe specific to said target, which correction makes said hybridization signal directly comparable to a hybridization signal provided by the binding of the same target of the reference sample labelled with the second label to the same capture probe specific to said target.  
           [0025]    In a preferred embodiment, the rRNA competitor probe is present in a concentration that is about 5 to about 100 times that of the capture probe.  
           [0026]    The rRNA-derived cDNA may be labelled by any suitable means, such as by 3′ addition of phosphate, or labelling with cyanines, biotin, digoxygenin, fluorescein, a dideoxynucleotide, an amine, a thiol, an azo (N 3 ) group or fluorine, or any other form of label.  
           [0027]    An array comprising a plurality of spotted cDNA capture probes for binding ribosomal nucleics, alone or in combination with the competitor ribosomal probe in a separate component are further objects of this invention. The method of the present invention is suitable for use in high-throughput screening experiments.  
           [0028]    It may be used for any type of array experiment, including but not limited to the identification of sequences found in the open reading frame of genes coding for transcription factors, such as c-Rel, E2F-1, Egr-1, ER, NFκB, p50, p53, Sp1 and YY1.  
           [0029]    Other objects, advantages and features of the present invention will become more apparent upon reading of the following non restrictive description of preferred embodiments thereof, given by way of example only with reference to the accompanying drawings. 
       
    
    
     BRIEF DESCRIPTION OF THE DRAWINGS  
       [0030]    In the appended drawings:  
         [0031]    [0031]FIG. 1: A summary view of the described technology. Any given pool of total cellular RNA is usually composed of 80% ribosomal RNA (rRNA) and 20% messenger RNA (mRNA) and small nuclear RNAs. mRNA (except for the histone genes) is polyadenylated while rRNA never is. Making cDNA from both types of RNA by reverse transcription is possible if using a poly dT primer for mRNA (producing mRNA-derived cDNA, shown by solid arrows) and a specific primer for rRNA (producing rRNA-derived cDNA, shown by dashed arrows). Analysis of mRNA by microarray using the constant rRNA as a standard is made difficult by the relative overabundance of rRNA relative to mRNA; this problem is circumvented by adding to the hybridization mix a rRNA competitor probe which has the same sequence as the microarray&#39;s rRNA-cDNA capture probe (both shown as lines marked with an “r”). By sequestering the excess rRNA-derived cDNA, the competitor probe brings down the level of hybridizable and hybridized rRNA-derived cDNA to usable levels.  
         [0032]    [0032]FIG. 2: Human ribosomal DNA complete repeating unit (GB accession number #U13360). ETS: externally transcribed spacer. ITS: internally transcribed spacer. IGS: intergenic spacer. The position of a few rRNA probes is shown.  
         [0033]    [0033]FIG. 3: Illustration of spotted DNA capture probes on the slide. The slide used for the described experiment carries 12 probe blocks, identified 1 to 12. In each block there are 7 rows and 16 columns of spots. Each DNA capture probe was spotted in duplicate in an adjacent column (i.e., all odd columns correspond to a duplicate column) so there are 8 different DNA probes in a column. There are a total of 1344 spots on the slide, corresponding to duplicates of 463 different DNA capture probes and 209 negative controls (no DNA probe).  
         [0034]    [0034]FIG. 4: Cohybridization of labelled cDNA from Jurkat (reference sample: Cy3-green) and Jurkat-TPA (test sample: Cy5-red). Ratio images exported from GenePix Pro 3.0 (Axon Instruments Inc.) as JPEG (or TIFF) files are 24-bit RGB color.  
         [0035]    [0035]FIG. 5: Cohybridization of labelled cDNA from Jurkat (Cy3-green) and Jurkat-TPA (Cy5-red). Five (5) ng of rRNA competitor probe 2 was added to the hybridization mix to compete for the hybridization of the rRNA-derived cDNA to the attached rRNA cDNA capture probe 2. Ratio images exported from GenePix Pro 3.0 (Axon Instruments Inc.) as JPEG (or TIFF) files are 24-bit RGB color.  
         [0036]    [0036]FIG. 6: Cohybridization of labelled cDNA from Jurkat (Cy3-green) and Jurkat-TPA (Cy5-red). Fifty (50) ng of rRNA competitor probe 2 was added to the hybridization mix to compete for the hybridization of the rRNA-derived cDNA to the attached rRNA cDNA capture probe 2 (which has the same sequence as rRNA competitor probe 2). Ratio images exported from GenePix Pro 3.0 (Axon Instruments Inc.) as JPEG (or TIFF) files are 24-bit RGB color.  
     
    
     DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT  
       [0037]    Glossary  
         [0038]    In order to provide a clear and consistent understanding of terms used in the present description, a number of definitions are herein provided.  
         [0039]    Array: In the context of this invention, an array is a set of different spotted DNA consisting of capture probes for target nucleic acids. Such an array is described in U.S. Pat. No. 5,700,637.  
         [0040]    Complementary DNA (cDNA): DNA that has been synthesized from RNA by the effect of the enzyme reverse transcriptase, converting RNA bases into their complements (A to T, U to A, G to C, C to G).  
         [0041]    Cy3, Cy5: Non-radioactive fluorescent dyes from Amersham Pharmacia Biotech that are widely used for labeling DNA in microarray experiments.  
         [0042]    Feature: A feature is a spot (typically of DNA) on a slide. The collection of such features is called a microarray.  
         [0043]    Hydridization : The process of joining two complementary strands of DNA, or one strand each of DNA and RNA, to form a double-stranded molecule.  
         [0044]    Messenger RNA (mRNA): RNA that is used to direct the protein synthesis that is part of gene expression. It represents but a small fraction of the total RNA found in a cell.  
         [0045]    mRNA-derived cDNA: cDNA synthesized from a mRNA template using reverse transcriptase and a mRNA-specific primer.  
         [0046]    Microarray-sequestered DNA or DNA capture probe: DNA (single-stranded or double-stranded) that are anchored onto the solid surface of a microarray. (See fuller description of microarrays immediately following this Glossary.)  
         [0047]    Oligonucleotide: A short strand of single-stranded DNA, typically composed of up to 50 bases.  
         [0048]    Pixel Intensity: The raw intensity of a pixel on a GenePix (Axon Instrument Inc.) single-wavelength or ratio image, falling in a range from 0 to 65535.  
         [0049]    PMT: Photomultiplier tubes in scanners used to analyze array images. These array images are the end products of comparative hybridization experiments.  
         [0050]    Ratio Image : The ratio image is an RGB (Red-Green-Blue) overlay image. In this image, wavelength #1 (635 nm) is mapped to the green channel of the RGB image, and wavelength #2 (532 nm) is mapped to the red channel. Superimposing these two images onto each other results in a third, composite image, whose color is a blend of the red and green signals.  
         [0051]    Ratio of medians: The ratio of medians is the ratio of the background subtracted median pixel intensity at the second wavelength to the background subtracted median pixel intensity at the first wavelength.  
         [0052]    Reference cDNA: this cDNA originates from a reference sample that is used for comparison with another one, called test cDNA obtained from a test sample. The reference cDNA serves as a control against which test cDNAs may be compared to quantify changes in the level of expression of any mRNA found in the test sample. Typically, the reference cDNA is labelled with Cy3-dCTP (green fluorescent label) when a fluorescent label is used.  
         [0053]    RGB: Red-Green-Blue color.  
         [0054]    Ribosomal RNA (rRNA): structural RNA found in the ribosomes. It is the most abundant form of RNA in the cell and does not vary significantly.  
         [0055]    rRNA-cDNA probe: a probe which is designed to hybridize to the rRNA-derived cDNA found in the hybridization mixture. This probe may be the capture probe, which may have the same sequence as the rRNA competitor probe (see below) so as to compete with it for the target rRNA-derived cDNA.  
         [0056]    rRNA competitor probe: a DNA oligonucleotide with the same sequence as part of a ribosomal RNA-cDNA sequence and capable of competing with the microarray capture probe for hybridization with a rRNA-derived cDNA. This oligonucleotide has the role of competing for the limited space available on the rRNA cDNA capture probe bound to the microarray, thus reducing the quantity of rRNA-derived cDNA which can be retained on the microarray and thus allowing the use of rRNA-derived cDNA as an &lt;&lt;internal standard&gt;&gt;.  
         [0057]    rRNA-derived cDNA: cDNA synthesized from a rRNA template using reverse transcriptase and a rRNA-specific primer.  
         [0058]    Saturation : Saturation refers to the overloading of the photodetection circuitry. Saturation can be reduced by reducing the amount of light that is reaching the PMTs, which is done by reducing the amount of incident laser light. In practice, this is accomplished by reducing the voltage of the PMT, which reduces its gain. Saturating pixels in GenePix 1.0 are shown as white pixels in the raw wavelength images.  
         [0059]    Spotted DNA: Known DNA capture probe that is spotted onto a microarray slide and used to identify the nucleic acids present in unknown samples (test and reference). The spotted DNA could be oligonucleotide or cDNA.  
         [0060]    Test cDNA: cDNA from a cell sample that is to be tested, in comparison with a reference sample. Typically, the test cDNA is labelled with Cy5-dCTP (red fluorescent label) when a fluorescent label is used.  
         [0061]    Microarrays are made from a collection of purified DNAs. A drop of each type of DNA in solution is placed onto a specially-prepared glass microscope slide by an arraying machine. The arraying machine can quickly produce a regular grid of thousands of spots in a square about 2 cm on a side, small enough to fit under a standard slide cover slip. The DNA in the spots is bound to the glass to keep it from washing off during the hybridization reaction. The choice of DNA to be used within the spots on a microarray&#39;s surface determines which genes can be detected in a comparative hybridization assay. These DNA probes could be synthetic oligonucleotides or PCR amplified DNA (hence the terms “oligo microarray” and “cDNA microarray”).  
         [0062]    The invention relates to rRNA used as an internal standard for the normalization of the fluorescence intensities in microarray analysis experiments. This can provide an estimate of relative abundance of multiple mRNAs and allow direct comparison between two RNA samples.  
         [0063]    Use of rRNA for normalization provides a sound method of identifying differentially expressed genes between two samples because its percentage of abundance in total RNA does not vary through the cell cycle or with a particular treatment.  
         [0064]    In order to detect the difference in gene expression between two samples on a single microarray slide, the RNA should be reverse transcribed to cDNA and labelled with two different fluorophores prior to cohybridizing both samples to the same slide and same spots simultaneously. There are several techniques that allow labeling of cDNA. Direct labeling is done by the incorporation of a fluorescent nucleotide such as, for example, Cy3-dCTP (green) or Cy5-dCTP (red) (from Amersham-Pharmacia Biotech), during the reverse transcription reaction. Other protocols may be used for labeling the cDNA following the reverse transcription reaction (indirect labeling). Alternatively, the cDNA can be used for RNA amplification involving T7 polymerase. This method relies on attaching a T7 promoter sequence to the reverse transcriptase primer used for synthesis of the first cDNA strand. After second strand cDNA synthesis, one can generate amplified RNA (aRNA) using T7 RNA polymerase and the double-stranded cDNA molecules as targets for the linear amplification. Those targets can then be labelled directly or indirectly.  
         [0065]    In the present invention, the reverse transcriptase reaction for the cDNA labeling step involves the use of two kinds of reverse transcriptase primers in the same reaction: an oligo-dT and specific primers for rRNA (5.8S, 1 8S or 28S rRNA). One set of RNA to be reverse transcribed is all the polyA+ mRNA that is present in the RNA sample, the other set is the rRNA. Both sets are labelled in the same sample with the same label. Random short primer like random hexamers or sets of specific primers could also be used as alternative methods to reverse transcribe all the polyA+ mRNA.  
         [0066]    In a typical experiment, the reference cDNA is labelled with Cy3 and the test cDNA is prepared in the presence of Cy5. Both of these cDNA populations are hybridized to the same spotted DNA capture probes on the microscope slide. After the hybridization and washing steps, the slide is scanned at the appropriate wavelengths and an image is generated for each wavelength. In the derived ratio image, a red spot indicates that the test cDNA for this feature is more abundant than the reference cDNA which means that the test cDNA is being expressed at a level higher than the reference cDNA; a yellow spot means that there is no change in the expression level between the two populations of test and reference cDNA. In order to measure changes in gene expression numerically, image analysis software like GenePix 1.0 (Axon Instruments, Inc.) extracts the intensity of a given feature (spot) from an image and performs a number of computations on the raw data. In this kind of comparative analysis, normalization is essential to compensate for variations in RNA isolation techniques, initial quantification errors, tube to tube variation in reverse transcriptase reactions and other experimental variations. That is where the present invention intervenes: normalization is possible upon correcting the green intensity and the red intensity of the spot having the internal standard capture probe to achieve a ratio of 1. This normalization therefore leads to the obtention of a correction factor that is applied to the intensities of signals specific to each reference and test samples.  
         [0067]    The end product of a comparative hybridization experiment is a scanned array image. Saturated pixels appear when there are more photons detected than can be processed by the photomultiplier tubes (PMT) of the scanner. This occurs when the amount of hybridized target per shot is too high. Saturated pixels cannot be used for proper measurement of the signal intensity. PMT should then be set to avoid the detection of saturated pixels. As a consequence, this reduces the signal intensity of all other spots and low levels of cDNA will not be detected.  
         [0068]    In the present invention, the hybridization step is performed with specific amounts of free rRNA-derived cDNA (competitor probe) added into the hybridization buffer so as to set up a competition for ribosomal cDNA of the test cDNA and of the reference cDNA (if the latter is part of the experiment) with the capture probe. For efficient competition, the competition probe should be nearly identical to the capture probe or have a high level of overlapping sequences therewith. The hybridization efficiency of the rRNA-derived cDNA with the capture probe can be predictably and reproducibly altered. Reducing the hybridization of these internal and abundant targets in microarray experiments has the effect of generating a signal intensity in the same dynamic range of detection as the less abundant targets in microarrays.  
         [0069]    The competition is important because the control must be detected at a level similar to the test transcript. If one target is present at a significantly higher concentration than the other, the PMT (laser voltage) has to be reduced to avoid a saturated signal, with the consequence of reducing all the other signals. The ability to obtain quantitative information for low abundant mRNA will then be lost.  
         [0070]    With the applicants&#39; invention, the normalization factor is computed using the ratio of intensity obtained between the signal detected for the test cDNA and that of the reference cDNA. This ratio should be 1.0. For example, if the ratio is 0.8, a normalization factor of 1.25 would have to be calculated (1/0.8). The analyzed data is then corrected using this factor. If the normalization factor is greater than 2 (or less than 0.5) the slide is usually rescanned with other PMT voltage to ensure maximum data integrity.  
         [0071]    Results  
         [0072]    The applicants used the products and protocols that are described herein, which results in proper normalization.  
         [0073]    [0073]FIG. 1 illustrates how a given sample (reference or test) is labelled and hybridized to capture probes (a plurality of specific cDNA probed spots and one internal standard probe spot). The labelled ribosomal cDNA is mixed with a competitor probe that is here identical to the capture probe.  
         [0074]    [0074]FIG. 2 illustrates the organization of the rDNA locus. The microarray was made from a collection of synthetic DNA oligonucleotides as DNA probes.  
         [0075]    [0075]FIG. 3 illustrates the positions of spotted DNA capture probes on the slide. In order to use the cDNA made from rRNA for normalisation, a DNA capture probe having a sequence that is complementary to the rRNA-derived cDNA has also been spotted on the array slide.  
         [0076]    Table 1 shows the sequences of two DNA-probes designed for that purpose. 3D-Link Activated slides from Surmodics Inc. were used according to the supplier&#39;s protocol for the covalent attachment of the 5′ amino modified oligonucleotides and prehybridization treatment of the slides. On the DNA microarray used here, each spot contains approximately 0.15 ng of bound DNA probe.  
         [0077]    The cDNA for microarray analysis was prepared from RNA templates by incorporation of fluorescent-labelled deoxyribonucleotides during first strand cDNA synthesis. 10 μg of total RNA extract from Jurkat and Jurkat-TPA cell lines (Geneka Biotechnology) was used. Priming of cDNA synthesis was performed using 2 μg of oligo (dT). For each labeling reaction, 50 ng of 18S primer were included to allow reverse transcription of the 18S rRNA. Table 1 shows the sequences of the 18S reverse transcriptase primer. In this experiment, labelled reference cDNA from Jurkat total RNA was prepared using Cy3-dCTP while Jurkat-TPA total RNA was reverse transcribed and labelled using Cy5-dCTP (Amersham Pharmacia Biotech) to produce labelled test cDNA. Reverse transcriptase reactions were performed using the Superscript II reverse transcriptase (LifeTechnologies) enzyme according to the supplier&#39;s protocol.  
         [0078]    For the hybridization and washing steps the following conditions were used (optimized conditions for 3D-Link Activated slides, Surmodics Inc.). Labelled cDNAs were cohybridized in 5×SSC-0.1% SDS buffer for 16 hours at 45° C. Washing was performed by incubating slides two times 15 minutes in 2×SSC-0.1% SDS at 45° C., one time 5 minutes in 0.2×SSC at room temperature and one time 5 minutes in 0.1×SSC at room temperature. Slides were dried by low speed centrifugation.  
         [0079]    The test and reference cDNAs were analyzed through hybridization with the microarray-sequestered cDNA. In this type of experiment, if the test or reference cDNA contains a sequence that is complementary to the DNA on a given spot, that cDNA will hybridize to the spot, where it will be detectable by virtue of its fluorescence.  
         [0080]    [0080]FIG. 4 shows a ratio image of a typical cohybridized cDNA with no internal standard according to the invention. The target cDNAs and the results are listed in Table 2 (see right column). FIGS. 5 and 6 show counterparts of arrays of FIG. 4 but with 5 ng and 50 ng of ribosomal competitor probe, respectively, in accordance with this invention. The results are listed in Table 2, in the middle and left columns, respectively.  
         [0081]    Saturated spots were observed for the two rRNA cDNA probes (DNA probe 1 and probe 2). The GenePix 3.0 software (Axon Instruments Inc.) was used to extract the intensity of each feature (hybridized spot) from the image. Table 2 shows the mean value of pixel intensity for each spot. To analyse feature intensity and calculate a ratio, the local background should be subtracted from the median value of the pixel. The method used by GenePix Pro 3.0 for determining the background intensity is a local background subtraction technique. A different background is therefore computed for each individual feature-indicator and the median value of the background pixel intensities are reported (Table 2).  
         [0082]    The end product of a comparative hybridization experiment is a scanned array image. Saturated pixels appear when there are more photons detected than the photomultiplier tubes (PMT) of the scanner can process. This occurs when the amount of hybridized cDNA to the spot is too high. Saturated pixels cannot be used for proper measurement of the signal intensity. PMT should then be set to avoid the detection of saturated pixels. As a consequence, this reduces the signal intensity of all other spots, and lower levels of cDNA will not be detected.  
         [0083]    Because of the high abundance of the rRNA-derived cDNA relatively to the mRNA-derived cDNA, it is important to reduce its hybridization to the microarray-sequestered DNA. In this invention, the applicants compete the hybridization of the rRNA-derived cDNA to the microarray DNA capture probe by adding a defined amount of rRNA competitor probe in the hybridization buffer, said probe carrying the same sequence as the microarray-bound probe. Five (5) to 100 molar excess of competitor probe relative to the quantity of microarray DNA capture probe is enough to obtain a rRNA-derived cDNA signal intensity in the same dynamic range of detection as the other cDNAs (i.e., test and/or reference mRNA-derived cDNA), which are otherwise present in much lesser quantities in the reaction buffer. The amount of molar excess to be used is essentially a function of the amount of the total RNA used for the assay (for example: 0.2 to 20 μg).  
         [0084]    In short, because of their relatively invariant expression across tissues and treatments, 18S and 28S RNA are ideal internal controls for quantitative RNA analysis by microarrays. The current invention describes how to use these rRNAs to that end by compensating, thanks to competition with specific oligos, for their overabundance relative to the mRNA of test and reference cell samples.  
         [0085]    The overall exhaustive results of comparison of test and reference cDNAs, normalized in accordance with the method and principles of the present invention, are provided in appendix 1.  
         [0086]    Although the present invention has been described hereinabove by way of preferred embodiments thereof, it can be modified, without departing from the spirit and nature of the subject invention, as defined in the appended claims.  
                                                     TABLE 1                                       Positions relative   Spotted position            Name   DNA sequences   to 5′ 18S sequence   Block   Column   Row               RT primer   CTTATGACCCGCACTTACTCG   5′-1667-1647-3′   —   —   —       DNA probe 1   CCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATA   5′-833-872-3′   8   1   5                   8   2   5                   1   11   6                   1   12   6       DNA probe 2   TCTCGATTCCGTGGGTGGTGGTGCATGGCCGTTCTTAGTT   5′-1308-1647-3′   10   1   5                   10   2   5                   3   11   6                   3   12   6                  
 
         [0087]    [0087]                                                                                                                                                                                                                                                                                                                                                 TABLE 2                                       Hybridization with 50 ug of probe 2 as competitor                Ratio of median value                                    Not                                           normalized   beta-actin   18 S   F635   F532       Block   Column   Row   Gene Name   Probe name   —   1.02   —   median   median                    8   1   5   18S   probe 1   1.04   1.02   undetectable   27678   26672       1   11   6   18S   probe 1   1.00   0.98   undetectable   65217   65349       1   12   6   18S   probe 1   1.00   0.98   undetectable   65217   65352       8   2   5   18S   probe 1   0.85   0.83   undetectable   21986   26060       10   1   6   18S   probe 2   0.93   0.91   undetectable   −73   33       10   2   6   18S   probe 2   1.27   1.25   undetectable   −31   10       3   12   6   18S   probe 2   1.00   0.98   undetectable   83   254       3   11   6   18S   probe 2   1.02   1.00   undetectable   122   285       5   7   6   Beta actin   actin 1   0.78   0.76   undetectable   1159   1791       5   8   6   Beta actin   actin 1   0.88   0.87   undetectable   977   1351       10   3   1   Beta actin   actin 1   0.87   0.85   undetectable   1674   2034       10   4   1   Beta actin   actin 1   0.89   0.87   undetectable   1880   2213       4   3   1   Beta actin   actin 1   0.63   0.62   undetectable   2010   3400       11   14   5   Beta actin   actin 1   0.86   0.84   undetectable   1607   1981       11   13   5   Beta actin   actin 1   0.91   0.89   undetectable   1760   2021       4   4   1   Beta actin   actin 1   0.68   0.67   undetectable   1833   2880       6   1   1   Beta actin   actin 2   0.96   0.94   undetectable   3619   3853       3   2   1   Beta actin   actin 2   0.88   0.86   undetectable   278   603       4   2   1   Beta actin   actin 2   0.81   0.80   undetectable   1667   2185       6   2   1   Beta actin   actin 2   1.00   0.98   undetectable   3013   3092       1   8   6   Beta actin   actin 2   0.75   0.73   undetectable   1641   2348       4   1   1   Beta actin   actin 2   0.75   0.73   undetectable   1651   2355       3   1   1   Beta actin   actin 2   0.93   0.91   undetectable   419   686       5   1   1   Beta actin   actin 2   0.87   0.86   undetectable   530   827       5   2   1   Beta actin   actin 2   0.79   0.77   undetectable   323   673       1   7   6   Beta actin   actin 2   0.76   0.75   undetectable   2157   2986       3   8   6   Beta actin   actin 3   1.41   1.38   undetectable   1765   1336       3   7   6   Beta actin   actin 3   1.26   1.23   undetectable   2079   1744       11   2   1   Beta actin   actin 3   1.51   1.48   undetectable   1697   1175       11   1   1   Beta actin   actin 3   1.50   1.47   undetectable   1852   1299       12   2   1   Beta actin   actin 3   1.22   1.19   undetectable   572   534       12   1   1   Beta actin   actin 3   1.13   1.11   undetectable   545   651       10   2   1   Beta actin   actin 3   1.11   1.09   undetectable   980   947       9   2   1   Beta actin   actin 3   1.23   1.21   undetectable   1173   1020       10   1   1   Beta actin   actin 3   0.92   0.90   undetectable   514   655       8   2   1   Beta actin   actin 3   1.28   1.25   undetectable   991   808       8   1   1   Beta actin   actin 3   1.36   1.34   undetectable   931   704       9   13   5   Beta actin   actin 3   1.28   1.25   undetectable   1379   1128       9   1   1   Beta actin   actin 3   1.43   1.40   undetectable   1330   976       9   14   5   Beta actin   actin 3   1.51   1.48   undetectable   1946   1303       2   1   1   Beta actin   actin 3   0.76   0.74   undetectable   1630   2269       2   2   1   Beta actin   actin 3   0.76   0.75   undetectable   1800   2462       4   2   4   9G8 splicing   L22253_B   0.69   0.68   undetectable   361   689       9   14   4   A-Myb   X13294_B   2.30   2.25   undetectable   197   64       4   8   4   ASH1   L08424_A   1.33   1.31   undetectable   587   487       3   5   3   BTEB   D31716_B   3.88   3.80   undetectable   332   33       3   12   5   BTF3 homologue   M90355_A   4.15   4.07   undetectable   1627   338       4   4   2   CBFA1/OSF2   AF053949_B   0.52   0.51   undetectable   −136   14       2   2   5   CDP   M74099_B   0.45   0.44   undetectable   −54   173       11   10   5   cyclin D1   AML 12   1.75   1.72   undetectable   4205   2401       6   6   4   EN2   L12700_B   2.93   2.88   undetectable   1517   476       8   15   6   GAPDH   S6-1   1.37   1.35   undetectable   2104   1553       2   10   2   GTF2IP1   AF036613_B   0.49   0.48   undetectable   −106   21       5   12   1   ZRP-1   AF000974_A   2.99   2.93   undetectable   4235   1405                        Hybridization with 5 ug of probe 2 as competitor                Ratio of median value                                    Not                                           normalized   beta-actin   18S   F635   F532       Block   Column   Row   Gene Name   Probe name   —   1.20   1.11   median   median                    8   1   5   18S   probe 1   0.73   0.61   0.66   5617   7877       1   11   6   18S   probe 1   0.77   0.65   0.70   50642   65367       1   12   6   18S   probe 1   0.68   0.56   0.61   28798   42677       8   2   5   18S   probe 1   0.79   0.66   0.71   4808   6252       10   1   6   18S   probe 2   1.19   0.99   1.07   1446   1275       10   2   6   18S   probe 2   1.24   1.03   1.12   1437   1211       3   12   6   18S   probe 2   1.01   0.84   0.92   2904   2973       3   11   6   18S   probe 2   0.99   0.82   0.89   2970   3112       5   7   6   Beta actin   actin 1   0.78   0.65   0.71   2778   3771       5   8   6   Beta actin   actin 1   0.81   0.67   0.73   2813   3723       10   3   1   Beta actin   actin 1   0.89   0.74   0.80   2114   2491       10   4   1   Beta actin   actin 1   0.95   0.60   0.86   1958   2142       4   3   1   Beta actin   actin 1   0.79   0.66   0.72   886   1246       11   14   5   Beta actin   actin 1   0.85   0.70   0.76   4081   4908       11   13   5   Beta actin   actin 1   0.82   0.68   0.74   4163   5178       4   4   1   Beta actin   actin 1   0.84   0.70   0.76   630   861       6   1   1   Beta actin   actin 2   1.34   1.12   1.21   6216   6179       3   2   1   Beta actin   actin 2   1.13   0.94   1.02   2734   2573       4   2   1   Beta actin   actin 2   1.07   0.89   0.97   3255   3107       6   2   1   Beta actin   actin 2   1.29   1.07   1.16   5016   3954       1   8   6   Beta actin   actin 2   0.90   0.75   0.81   5528   6304       4   1   1   Beta actin   actin 2   0.86   0.72   0.78   3905   4676       3   1   1   Beta actin   actin 2   1.13   0.95   1.02   6154   5479       5   1   1   Beta actin   actin 2   0.97   0.81   0.88   2991   3266       5   2   1   Beta actin   actin 2   0.80   0.67   0.72   1924   2563       1   7   6   Beta actin   actin 2   0.93   0.78   0.84   8491   9183       3   8   6   Beta actin   actin 3   1.38   1.15   1.25   7582   5556       3   7   6   Beta actin   actin 3   1.46   1.22   1.32   9368   6469       11   2   1   Beta actin   actin 3   1.73   1.44   1.56   1674   996       11   1   1   Beta actin   actin 3   1.83   1.53   1.66   2150   1173       12   2   1   Beta actin   actin 3   1.31   1.09   1.18   4607   3517       12   1   1   Beta actin   actin 3   1.28   1.07   1.16   4478   3494       10   2   1   Beta actin   actin 3   1.18   0.99   1.07   1003   920       9   2   1   Beta actin   actin 3   1.65   1.37   1.49   7356   4461       10   1   1   Beta actin   actin 3   1 26   1.05   1.14   5499   4379       8   2   1   Beta actin   actin 3   1.69   1.41   1.52   1957   1167       8   1   1   Beta actin   actin 3   1.60   1.33   1.44   1998   1288       9   13   5   Beta actin   actin 3   1.67   1.39   1.50   4283   2609       9   1   1   Beta actin   actin 3   1.70   1.41   1.53   8913   5248       9   14   5   Beta actin   actin 3   1.60   1.33   1.44   2481   1579       2   1   1   Beta actin   actin 3   1.18   0.98   1.06   986   905       2   2   1   Beta actin   actin 3   1.13   0.94   1.02   4407   3937       4   2   4   9G8 splicing   L22253_B   0.98   0.82   0.89   777   875       9   14   4   A-Myb   X13294_B   2.73   2.28   2.47   1228   429       4   8   4   ASH1   L08424_A   1.49   1.24   1.35   1332   908       3   5   3   BTEB   D31716_B   2.86   2.38   2.58   1565   510       3   12   5   BTF3 homologue   M90355_A   3.47   2.89   3.13   3479   1036       4   4   2   CBFA1/OSF2   AF053949_B   1.25   1.04   1.13   62   99       2   2   5   CDP   M74099_B   0.79   0.66   0.72   138   296       11   10   5   cyclin D1   AML 12   1.60   1.33   1.45   11710   7312       6   6   4   EN2   L12700_B   3.61   3.01   3.26   1835   458       8   15   6   GAPDH   S6-1   2.15   1.79   1.94   3462   1593       2   10   2   GTF2IP1   AF036613_B   0.66   0.57   0.62   −45   83       5   12   1   ZRP-1   AF000974_A   3.24   2.70   2.92   12043   3689                        Hybridization without competitor                Ratio of median value                                    Not                                           normalized   beta-actin   18 S   F635   F532       Block   Column   Row   Gene Name   Probe name   —   0.56   —   median   median                    8   1   5   18S   probe 1   1.01   1.80   saturated   65181   65226       1   11   6   18S   probe 1   1.01   1.80   saturated   65181   65226       1   12   6   18S   probe 1   1.01   1.80   saturated   65160   65187       8   2   5   18S   probe 1   1.01   1.80   saturated   65154   65211       10   1   6   18S   probe 2   1.01   1.80   saturated   65250   65274       10   2   6   18S   probe 2   1.01   1.80   saturated   65250   65283       3   12   6   18S   probe 2   1.01   1.80   saturated   65157   65199       3   11   6   18S   probe 2   1.01   1.80   saturated   65115   65168       5   7   6   Beta actin   actin 1   0.66   1.18   saturated   42650   65208       5   8   6   Beta actin   actin 1   0.60   1.07   saturated   32564   54998       10   3   1   Beta actin   actin 1   0.54   0.96   saturated   31689   59418       10   4   1   Beta actin   actin 1   0.50   0.89   saturated   20804   42413       4   3   1   Beta actin   actin 1   0.52   0.93   saturated   5227   10326       11   14   5   Beta actin   actin 1   0.57   1.02   saturated   5227   9416       11   13   5   Beta actin   actin 1   0.57   1.02   saturated   4828   8663       4   4   1   Beta actin   actin 1   0.47   0.85   saturated   3316   7269       6   1   1   Beta actin   actin 2   0.61   1.10   saturated   12776   21111       3   2   1   Beta actin   actin 2   0.60   1.07   saturated   11482   19359       4   2   1   Beta actin   actin 2   0.56   1.00   saturated   9879   18018       6   2   1   Beta actin   actin 2   0.62   1.10   saturated   8311   13731       1   8   6   Beta actin   actin 2   0.56   1.01   saturated   8060   14583       4   1   1   Beta actin   actin 2   0.50   0.89   saturated   6632   13645       3   1   1   Beta actin   actin 2   0.56   1.00   saturated   5885   10732       5   1   1   Beta actin   actin 2   0.51   0.92   saturated   4246   8568       5   2   1   Beta actin   actin 2   0.50   0.89   saturated   3917   8126       1   7   6   Beta actin   actin 2   −0.91   −1.63   saturated   −206   −149       3   8   6   Beta actin   actin 3   0.72   1.28   saturated   12612   17918       3   7   6   Beta actin   actin 3   0.65   1.16   saturated   10632   16662       11   2   1   Beta actin   actin 3   0.87   1.55   saturated   9874   11511       11   1   1   Beta actin   actin 3   0.93   1.66   saturated   8951   9743       12   2   1   Beta actin   actin 3   0.66   1.18   saturated   7276   11204       12   1   1   Beta actin   actin 3   0.61   1.09   saturated   7196   11985       10   2   1   Beta actin   actin 3   0.54   0.97   saturated   6401   12065       9   2   1   Beta actin   actin 3   0.67   1.20   saturated   5666   8611       10   1   1   Beta actin   actin 3   0.53   0.94   saturated   5565   10881       8   2   1   Beta actin   actin 3   0.79   1.42   saturated   4425   5686       8   1   1   Beta actin   actin 3   0.66   1.19   saturated   4266   6610       9   13   5   Beta actin   actin 3   0.62   1.11   saturated   3873   6437       9   1   1   Beta actin   actin 3   0.70   1.26   saturated   3211   4705       9   14   5   Beta actin   actin 3   0.62   1.10   saturated   2984   5021       2   1   1   Beta actin   actin 3   0.48   0.86   saturated   2319   5083       2   2   1   Beta actin   actin 3   0.44   0.79   saturated   2317   5572       4   2   4   9G8 splicing   L22253_B   0.48   0.86   saturated   1217   2852       9   14   4   A-Myb   X13294_B   0.84   1.50   saturated   664   877       4   8   4   ASH1   L08424_A   0.70   1.25   saturated   3104   4657       3   5   3   BTEB   D31716_B   1.18   2.10   saturated   3709   3172       3   12   5   BTF3 homologue   M90355_A   1.14   2.03   saturated   5707   5036       4   4   2   CBFA1/OSF2   AF053949_B   0.51   0.91   saturated   219   754       2   2   5   CDP   M74099_B   0.32   0.57   saturated   88   743       11   10   5   cyclin D1   AML 12   1.03   1.84   saturated   15590   15215       6   6   4   EN2   L12700_B   1.41   2.51   saturated   7429   5251       8   15   6   GAPDH   S6-1   0.43   0.76   saturated   3632   9331       2   10   2   GTF2IP1   AF036613_B   0.36   0.65   saturated   20   458       5   12   1   ZRP-1   AF000974_A   1.61   2.88   saturated   13359   8293                    
         [0088]    Appendix 1: Signal normalization using 18S RNA as an internal standard. Two microarray analyses were performed independently, each one comparing the expression of many transcription factors in Jurkat cells and in Jurkat cells treated with the phorbol ester TPA. The signals obtained in the latter case were divided by the signals obtained in the former case to get a ratio of induction by TPA in these cells. The signals were normalized using 18S RNA as a standard (see columns 3 and 4). Since 18S RNA is used as a control in both experiments and that the same type of cells were used, presumably giving very similar results, the ratio of the results obtained in each experiment should be nearing 1. That ratio is presented in column 5.  
                                                                             Column 3                       Jurkat/Jurkat   Column 4   Column 5           Column 2   TPA   Jurkat/Jurkat   Ratio of       Column 1   Accession   ratio   TPA ratio   experiments       Gene name   number   experiment 1   experiment 2   1 and 2                                9G8 splicing factor   L22253   0.84   1.00   0.836078512       9G8 splicing factor   L22253   0.77   0.99   0.779340183       A-Myb   X66087   1.32   1.38   0.950679679       A-Myb   X66087   1.34   1.43   0.937305665       A-Myb   X13294   1.12   1.21   0.924150275       A-Myb   X13294   1.12   1.21   0.924083463       ABF-1   AF060154   0.45   0.39   1.166895465       ABF-1   AF060154   0.39   0.38   1.029207795       ABH   NM_006020   0.91   1.05   0.865303363       ABH   NM_006020   0.81   0.98   0.822950019       ABP/ZF   U82613   1.32   1.64   0.804108596       ABP/ZF   U82613   1.25   1.60   0.783304597       AF10   NM_004641   1.24   1.31   0.947593818       AF10   NM_004641   1.23   1.32   0.931357689       AIB3   AF208227   1.33   1.28   1.034779297       AIB3   NM_014071   1.09   1.25   0.870698314       AIB3   NM_014071   1.07   1.36   0.784035932       AIB3   AF208227   1.10   1.40   0.782294079       ALL-1   U04737   1.65   1.88   0.880126672       ALL-1   U04737   1.58   1.88   0.838592996       ALL-1   L04284   0.66   0.79   0.838134698       AML2   Z35278   0.44   0.51   0.858684813       AML2   Z35278   0.42   0.55   0.77112205       AML3   AF001450   1.28   1.32   0.974983445       AML3   AF001450   1.34   1.39   0.966458433       AP-2gamma   U85658   2.57   2.62   0.978390776       AP-2gamma   U85658   2.23   2.59   0.86381938       AP-4   X57435   1.21   1.23   0.984438472       AP-4   X57435   1.17   1.28   0.91144528       AP4   NM_014374   1.39   1.59   0.871879245       AP4   NM_014374   1.32   1.59   0.831996755       APBB1   NM_001164   0.95   0.97   0.984113563       APBB1   NM_001164   0.79   0.99   0.801180869       APC   M74088   1.50   1.31   1.148676257       APC   M74088   1.29   1.46   0.8859936       APECED   AB006682   1.49   1.56   0.957659838       APECED   AB006682   1.38   1.65   0.837168643       APEX   NM_001641   0.88   1.13   0.783250131       APEX   NM_001641   0.84   1.08   0.780343345       APOBEC2   NM_006789   1.15   1.12   1.031439776       APOBEC2   NM_006789   1.04   1.05   0.990111417       APPL   NM_012096   1.32   1.54   0.856820461       APPL   NM_012096   1.31   1.56   0.839878811       AR   NM_000044   1.74   2.04   0.855879355       AR   NM_000044   1.60   2.01   0.796494966       ARNT   M69238   1.25   1.42   0.880056649       ARNT   M69238   1.24   1.42   0.876705905       ARNT   Y18500   0.78   0.96   0.816130578       ASH2L2   AF056717   1.34   1.35   0.994678817       ASH2L2   AF056717   1.38   1.40   0.991252318       ATBF1   NM_006885   0.90   1.01   0.889758762       ATBF1   NM_006885   0.90   1.02   0.879456944       ATF   D90209   1.05   1.01   1.035713928       ATF   D90209   0.97   1.01   0.960323304       ATF-a   X52943   1.54   1.88   0.817277421       ATF-a   X52943   1.51   1.93   0.780957523       ATF1   NM_005171   0.84   0.91   0.927916867       ATF1   NM_005171   0.87   1.02   0.854281302       ATF6   NM_007348   1.29   1.29   1.00327664       ATF6   NM_007348   1.09   1.28   0.856533977       BACH1   NM_001186   1.49   1.31   1.137064444       BACH1   NM_001186   1.45   1.62   0.891057108       BAPX1   NM_001189   2.55   2.33   1.093826453       BAPX1   NM_001189   2.46   2.59   0.946872482       BARX2   NM_003658   1.17   1.27   0.917084438       BARX2   NM_003658   1.14   1.37   0.830998058       BCL2   NM_000633   1.43   1.65   0.866945304       BCL2   NM_000633   1.37   1.70   0.806442848       BCL3   U05822   1.11   1.26   0.877431885       BCL3   M31732   1.17   1.38   0.848343893       BCL3   M31732   1.13   1.37   0.825031918       BCL3   U05822   1.02   1.30   0.790257156       Beta-actin   X00351   1.02   1.19   0.855958172       Beta-actin   X00351   1.02   1.21   0.843968769       Beta-actin   X00351   1.01   1.21   0.837209294       Beta-actin   X00351   1.00   1.19   0.836410947       beta-catenin   X89593   2.01   2.06   0.977986591       beta-catenin   X89593   1.99   2.11   0.942592932       BF-2   X74143   1.28   1.38   0.931388014       BF-2   X74143   1.22   1.37   0.894927517       BFP/ZNF179   AB026054   1.33   1.32   1.005754548       BFP/ZNF179   AB026054   1.36   1.37   0.993222418       BIRC4   NM_001167   1.51   1.44   1.054435009       BIRC4   NM_001167   1.40   1.50   0.932289706       BMZF3   NM_005773   0.92   1.08   0.850837495       BMZF3   NM_005773   0.90   1.13   0.798215326       brahma   X72889   5.90   5.49   1.074544412       brahma   X72889   5.14   5.97   0.86166573       BRCA2   NM_000059   1.45   1.75   0.824507422       BRCA2   NM_000059   1.39   1.74   0.798236353       Brn-3B   U06233   1.48   1.37   1.078166711       Brn-3B   U06233   1.47   1.50   0.974841891       Brn-4   X82324   1.57   1.06   1.486851514       Brn-4   X82324   1.29   1.07   1.198217087       BRS3   NM_001727   2.71   2.75   0.983814035       BRS3   NM_001727   2.36   2.77   0.851828571       BTEB   D31716   4.86   4.21   1.153934489       BTEB   D31716   4.30   4.32   0.995197771       BTEB2   D14520   1.25   1.27   0.978590601       BTEB2   D14520   1.30   1.39   0.933625786       BTF3   NM_001207   1.05   1.10   0.955111894       BTF3   NM_001207   0.99   1.08   0.913787418       BTF3a   M90352   2.83   2.32   1.219855319       BTF3a   M90352   2.70   2.39   1.130461687       BTF3L1   NM_001208   1.22   1.07   1.137813523       BTF3L1   NM_001208   1.16   1.05   1.102860167       BTF3L3   M90356   1.44   1.37   1.049188317       BTF3L3   M90356   1.24   1.34   0.927268611       bZip protein B-ATF   U15460   1.07   1.14   0.9426678       bZip protein B-ATF   U15460   0.97   1.08   0.901877866       c-Ets-1   X14798   1.09   1.25   0.873492353       c-Ets-1   X14798   1.10   1.32   0.830363686       c-maf   AF055376   5.74   4.79   1.19705637       c-maf   AF055376   4.91   5.10   0.962031195       c-Rel   M11595   1.33   1.41   0.946493027       c-Rel   X75042   1.32   1.46   0.902036285       c-Rel   M11595   1.27   1.42   0.889929469       c-Rel   X75042   1.14   1.47   0.777782886       C2H2 ZNF   AF033199   1.07   1.14   0.938338671       C2H2 ZNF   AF033199   0.99   1.16   0.852890579       C2H2-type ZNF   U95991   1.19   1.01   1.173282928       C2H2-type ZNF   U95991   0.98   1.04   0.942590144       C2ORF3   NM_003203   1.46   1.22   1.196699322       C2ORF3   NM_003203   1.01   0.93   1.093811577       CBF (5)   M37197   4.06   4.25   0.956014195       CBF (5)   M37197   3.60   4.09   0.88090602       CBF1   AF098297   1.61   1.63   0.991664197       CBF1   AF098297   1.38   1.78   0.772546908       CBFA1   L40992   1.30   1.45   0.898057655       CBFA1   L40992   1.26   1.46   0.865127809       CBFA1/OSF2   AF053949   1.22   1.28   0.951727989       CBFA1/OSF2   AF053949   1.22   1.33   0.92146037       CBFA2T1   NM_004349   1.49   1.65   0.901008111       CBFA2T1   NM_004349   1.24   1.59   0.780002118       CBFB   L20298   2.33   2.74   0.851333501       CBFB   L20298   2.36   2.91   0.8088749       CDP   M74099   1.39   1.61   0.85914075       CDP   M74099   1.27   1.64   0.77621359       CEBPB   NM_005194   1.24   1.47   0.846246886       CEBPB   NM_005194   1.26   1.49   0.846246188       CEBPD   NM_005195   0.83   1.00   0.829917576       CEBPD   NM_005195   0.84   1.03   0.822579365       CEBPE   U48866   1.91   2.01   0.948532903       CEBPE   U48866   2.06   2.38   0.86669978       CEZANNE   NM_020205   2.88   2.96   0.974633442       CEZANNE   NM_020205   2.65   2.83   0.935357017       CHD1   NM_001270   1.62   1.59   1.014951939       CHD1   NM_001270   1.43   1.59   0.898362477       CHD4   NM_001273   1.54   1.70   0.909055986       CHD4   NM_001273   1.49   1.72   0.862018232       CHFR   NM_018223   4.35   4.43   0.982194772       CHFR   NM_018223   3.92   4.36   0.899117503       CHN1   NM_001822   1.42   1.53   0.927629676       CHN1   NM_001822   1.37   1.49   0.923095091       CIS4   NM_004232   1.67   1.79   0.935688257       CIS4   NM_004232   1.82   2.13   0.851569476       CITED1   NM_004143   1.10   1.30   0.850853943       CITED1   NM_004143   1.17   1.39   0.844249881       CNBP   M28372   0.67   0.54   1.233592517       CNBP   M28372   0.62   0.54   1.163359863       coactivator EBV nuclear   U22055   0.82   0.94   0.869546763       protein 2       coactivator EBV nuclear   U22055   0.81   1.00   0.810099254       protein 2       COPEB   NM_001300   1.14   1.29   0.885046712       COPEB   NM_001300   1.12   1.34   0.833843243       COPS5   NM_006837   2.46   2.14   1.148421053       COPS5   NM_006837   2.48   2.32   1.071355007       CP2   U01965   1.01   1.23   0.82004865       CP2   U01965   1.00   1.30   0.771414141       CR53   AF017433   1.33   1.33   0.997732351       CR53   AF017433   1.29   1.39   0.925956448       CRE-BP1   J05623   1.13   1.38   0.819277436       CRE-BP1   J05623   1.02   1.26   0.815059942       CREB   M27691   0.92   1.09   0.842697518       CREB   M27691   0.85   1.06   0.7964146       CREBBP   NM_004380   1.09   1.25   0.872661186       CREBBP   NM_004380   1.12   1.30   0.86705145       CREBPA   NM_004904   1.26   1.30   0.971711147       CREBPA   NM_004904   1.10   1.24   0.887551154       CROC4   NM_006365   1.15   1.25   0.926055212       CROC4   NM_006365   1.16   1.38   0.842320854       CRSP70   NM_004831   0.91   1.06   0.854668195       CRSP70   NM_004831   0.92   1.15   0.803384327       CRSP9   NM_004270   1.37   1.49   0.919973517       CRSP9   NM_004270   1.40   1.53   0.919262135       CSDA   NM_003651   2.00   2.09   0.956497534       CSDA   NM_003651   1.79   2.09   0.857935728       CSPG4   NM_001897   6.91   6.16   1.121744511       CSPG4   NM_001897   6.24   6.25   0.998642122       cyclin T1   AF048730   1.27   1.54   0.823279433       cyclin T1   AF048730   1.20   1.47   0.813677962       cyclin T2a   AF048731   1.50   1.54   0.973727374       cyclin T2a   AF048731   1.65   1.70   0.971786333       Daxx   AB015051   1.22   1.49   0.814149894       Daxx   AB015051   1.16   1.45   0.796739358       DB1   D28118   1.21   1.38   0.873780256       DB1   D28118   1.20   1.38   0.871224304       DDXBP1   NM_016166   1.20   1.32   0.908250709       DDXBP1   NM_016166   1.14   1.32   0.865664426       DED   AJ249940   0.85   0.90   0.947823489       DED   AJ249940   0.84   0.90   0.93599742       DEK   S89712   1.38   1.62   0.856330516       DEK   S89712   1.32   1.55   0.852478465       DFFB   NM_004402   1.36   1.40   0.968276574       DFFB   NM_004402   1.22   1.55   0.787420865       DIP1   NM_012142   1.39   1.14   1.217929208       DIP1   NM_012142   1.17   1.15   1.01617335       DLC1   NM_006094   3.06   3.29   0.931248269       DLC1   NM_006094   2.97   3.29   0.903164687       DLX3   NM_005220   1.13   1.26   0.894141987       DLX5   NM_005221   1.45   1.39   1.04166642       DLX5   NM_005221   1.25   1.61   0.775477519       DMAHP   X84813   1.10   1.29   0.851587242       DMAHP   X84813   1.08   1.31   0.825399746       DMRT1   AJ276801   1.41   1.41   1.002793104       DMRT1   AJ276801   1.43   1.48   0.961743556       DNA-binding protein   X60824   1.36   1.52   0.897844438       DNA-binding protein   X60824   1.32   1.48   0.88927803       DNASE1   NM_005223   1.21   1.25   0.964151008       DNASE1   NM_005223   0.97   1.21   0.798481304       DNASE2   NM_001375   2.98   3.43   0.867988126       DNASE2   NM_001375   2.89   3.55   0.815129956       DRA   NM_000111   1.26   1.39   0.904139999       DRA   NM_000111   1.21   1.41   0.862444488       DREAM   AJ131730   0.78   0.96   0.819901761       DREAM   AJ131730   0.76   0.98   0.770874238       E2F1   M96577   0.89   1.03   0.869321414       E2F1   M96577   0.91   1.05   0.867695906       EAR-1r   D16815   2.06   2.10   0.984212792       EAR-1r   D16815   1.88   2.21   0.850783292       EGR1   X52541   1.47   1.50   0.979883348       EGR1   X52541   1.44   1.51   0.953589751       EGR1   M17254   0.86   1.03   0.832083695       EGR1   M17254   0.87   1.05   0.827505943       EGR4   NM_001965   0.60   0.71   0.840382873       EGR4   NM_001965   0.63   0.81   0.775954581       EKLF   U65404   0.98   1.04   0.944031465       EKLF   U65404   0.96   1.03   0.935317019       ELF1   M82882   1.76   1.83   0.964878433       ELF1   M82882   1.62   1.76   0.921751518       ELF4   NM_001421   1.45   1.41   1.027947336       ELF4   NM_001421   1.36   1.37   0.991044834       ELK3   NM_005230   1.28   1.57   0.815739725       ELK3   NM_005230   1.33   1.68   0.790796088       ELL   NM_006532   0.95   1.16   0.822566492       ELL   NM_006532   0.95   1.16   0.819455294       elongation factor 1-   X16869   1.35   1.50   0.8947725       alpha       elongation factor 1-   X16869   1.36   1.59   0.853485168       alpha           L34587   1.41   1.64   0.861800291       elongation factor SIII       elongation factor SIII   L34587   1.49   1.82   0.820065033       elongation factor-1-   Z21507   0.81   0.99   0.81190776       delta       elongation factor-1-   Z21507   0.78   1.00   0.782148893       delta       EN1   L12698   1.36   1.45   0.935865444       EN1   L12698   1.23   1.47   0.836794344       EPAS1   NM_001430   1.18   1.38   0.856844874       EPAS1   NM_001430   1.15   1.46   0.783761416       ERCC2   X52222   5.72   4.80   1.193231705       ERCC2   X52222   5.33   4.73   1.127089247       ERCC3   NM_000122   1.36   1.57   0.863467286       ERCC3   NM_000122   1.30   1.60   0.812147676       ERF-2   X78992   2.14   2.41   0.889330713       ERF-2   X78992   2.26   2.55   0.883602051       ERG   NM_004449   1.62   1.42   1.142428678       ERG   NM_004449   1.49   1.50   0.996969892       ERM   X96375   4.16   4.29   0.969559654       ERM   X96375   3.27   3.55   0.921520209       ERT   AF017307   2.43   2.68   0.90894817       ERT   AF017307   2.51   2.82   0.891141057       ESRRG   NM_001438   0.95   1.13   0.839582135       ESRRG   NM_001438   0.95   1.15   0.821231854       ETR101   NM_004907   2.74   2.75   0.997375352       ETR101   NM_004907   2.49   2.80   0.887790293       Ets transcription factor   AF115403   1.14   1.31   0.87442124       ESE-2b       Ets transcription factor   AF115403   1.11   1.43   0.77156259       ESE-2b       Ets-1 gene   AF193068   1.21   1.38   0.874625305       Ets-1 gene   AF193068   1.22   1.40   0.868962372       Ets-like   U30174   1.40   1.23   1.131217765       Ets-like   U30174   1.49   1.35   1.098811633       Ets-like   Z49980   1.61   1.51   1.067048232       Ets-like   Z49980   1.54   1.56   0.991710772       Ets2   M30137   1.75   2.02   0.86945137       Ets2   M30137   1.78   2.11   0.844919404       ETV1   NM_004956   1.13   1.25   0.910122678       ETV1   NM_004956   1.39   1.59   0.871215971       ETV6   U45432   1.38   1.43   0.965065589       ETV6   NM_001987   0.90   1.11   0.811726255       Evi-1   S82592   2.53   2.10   1.208239627       Evi-1   S82592   2.26   2.15   1.055074375       EWSR1   NM_005243   1.01   1.28   0.789906804       EWSR1   NM_005243   1.00   1.28   0.783731221       EZH2   U61145   1.26   1.35   0.932953273       EZH2   U61145   1.27   1.39   0.907474288       FACTP140   NM_007192   1.43   1.48   0.96265369       FACTP140   NM_007192   1.41   1.48   0.954817504       Fas-binding protein   AF015956   0.90   1.08   0.833884369       Daxx       Fas-binding protein   AF015956   0.89   1.09   0.81465638       Daxx       FBW1A   AF129530   1.31   1.45   0.900471742       FBW1A   AF129530   1.27   1.54   0.829306514       FGD1   U11690   1.33   1.14   1.173441119       FGD1   U11690   1.21   1.23   0.990554056       FGR   NM_005248   1.33   1.58   0.839283541       FGR   NM_005248   1.27   1.60   0.790883893       FHL1   AF110763   1.56   1.77   0.88200997       FHL1   AF110763   1.45   1.76   0.822210318       FKHL7   AF048693   3.42   3.29   1.040543697       FKHL7   AF048693   3.65   3.62   1.006927826       FKHR   AF032885   2.42   2.08   1.161966778       FKHR   AF032885   2.36   2.18   1.082816723       FKHRL1P1   AF032887   1.42   1.54   0.924383924       FKHRL1P1   AF032887   1.46   1.60   0.912174436       FLI_CDNA   AL360183   1.33   1.28   1.036167415       FLI_CDNA   AL360183   1.37   1.37   0.996443864       FLJ10173   NM_018014   1.04   1.04   0.999229429       FLJ10173   NM_018014   1.01   1.01   0.996944727       FLJ10251   NM_018039   1.31   1.43   0.911977997       FLJ10251   NM_018039   1.31   1.46   0.897214657       FLJ10339   NM_018063   1.62   1.87   0.866263178       FLJ10339   NM_018063   1.53   1.86   0.822236451       FLJ10469   NM_018102   0.94   1.09   0.865336872       FLJ10469   NM_018102   0.94   1.09   0.865236102       FLJ10688   AK001550   0.97   1.11   0.881574929       FLJ10688   AK001550   0.95   1.19   0.802514491       FLJ10891   NM_018260   1.22   1.31   0.928051813       FLJ10891   NM_018260   1.15   1.38   0.83802715       FLJ10909   AK001771   2.36   2.38   0.988865574       FLJ10909   AK001771   2.19   2.39   0.917728349       FLJ11015   NM_018300   1.10   1.19   0.922727928       FLJ11015   NM_018300   0.99   1.17   0.845365497       FLJ11137   NM_018337   1.43   1.64   0.875337744       FLJ11137   NM_018337   1.33   1.60   0.831187459       FLJ11340   AK002202   3.74   3.96   0.944037815       FLJ11340   AK002202   3.72   4.02   0.925252175       FLJ11344   AK002206   1.11   1.24   0.900786005       FLJ11344   AK002206   1.22   1.39   0.879708376       FLJ11688   AK021750   1.31   1.41   0.925531252       FLJ11688   AK021750   1.35   1.50   0.901037884       FLJ12606   AK022668   1.11   1.15   0.965529216       FLJ12606   AK022668   0.96   1.10   0.876202729       FLJ12628   AK022690   1.30   1.38   0.938935506       FLJ12628   AK022690   1.25   1.36   0.925116959       FLJ12644   AK000909   0.98   1.09   0.901825689       FLJ12644   AK000909   1.02   1.16   0.874104763       FLJ13479   AK023541   1.12   1.35   0.830838509       FLJ13479   AK023541   1.05   1.27   0.825925564       FLJ20337   NM_017772   1.55   1.60   0.969110576       FLJ20337   NM_017772   1.60   1.66   0.966477023       FLJ20428   AK000435   1.00   1.13   0.88699187       FLJ20428   AK000435   1.03   1.16   0.883146291       FLJ20438   ak000445   2.61   2.97   0.876697181       FLJ20438   ak000445   2.41   2.99   0.807812353       FLJ22332   AK025985   1.37   1.67   0.823105199       FLJ22332   AK025985   1.22   1.52   0.80219778       FLJ22973   AK026626   0.93   1.11   0.841359026       FLJ22973   AK026626   0.94   1.14   0.825377156       FOG2   NM_012082   1.03   1.10   0.930301277       FOG2   NM_012082   1.11   1.24   0.901732208       FOSL2   NM_005253   1.42   1.73   0.818161857       FOSL2   NM_005253   1.40   1.80   0.775807396       FOXD2   NM_004474   1.36   1.49   0.918399567       FOXD2   NM_004474   1.35   1.48   0.912187342       FOXD3   NM_012183   1.67   1.55   1.072311149       FOXD3   NM_012183   1.55   1.63   0.952188792       FOXO3A   NM_001455   0.87   1.10   0.789948212       FOXO3A   NM_001455   0.85   1.09   0.780082817       FRA-1   X16707   1.19   1.22   0.975373174       FRA-1   X16707   1.15   1.25   0.920368654       FREAC1   U13219   1.33   1.44   0.920850002       FREAC1   U13219   1.33   1.47   0.900355759       FREAC10   AF042831   1.37   1.53   0.895510594       FREAC10   AF042831   1.29   1.49   0.862685753       FREAC6   L13203   0.68   0.76   0.894745854       FREAC6   L13203   0.65   0.75   0.865206105       FREAC7   U13225   0.82   0.70   1.159351607       FREAC7   U13225   0.70   0.72   0.971169803       frpHE   AF026692   1.02   1.11   0.917414227       frpHE   AF026692   0.99   1.17   0.852068204       GABPB1   NM_005254   1.74   1.77   0.98532103       GABPB1   NM_005254   1.74   1.82   0.956282084       GADD 153   s40706   1.28   1.47   0.871741003       GADD 153   s40706   1.09   1.42   0.76973024       GAPDH   M33197   0.58   0.61   0.949162972       GAPDH   M33197   0.56   0.59   0.947048611       GCMA   NM_003643   1.20   1.32   0.908325507       GCMA   NM_003643   1.15   1.32   0.870108289       GCN5L1   NM_001487   0.80   0.93   0.856784201       GCN5L1   NM_001487   0.73   0.90   0.820087548       GIOT-1   AB021641   1.29   1.45   0.884372648       GIOT-1   AB021641   1.22   1.50   0.812297818       GIOT-2   NM_016264   0.93   1.07   0.868101488       GIOT-2   NM_016264   0.91   1.10   0.82720992       GIOT-3   NM_016265   0.87   0.97   0.893216374       GIOT-3   NM_016265   0.86   0.97   0.884789805       GIOT-4   NM_016266   1.73   2.15   0.806073313       GIOT-4   NM_016266   1.78   2.27   0.783305867       GLI   X07384   1.34   1.32   1.019171414       GLI   X07384   1.28   1.34   0.958829722       GLI3   M57609   2.18   1.98   1.098071683       GLI3   M57609   1.95   2.06   0.944192578       GPX5   NM_001509   0.94   1.08   0.865100605       GPX5   NM_001509   1.37   1.62   0.847040407       GRLF1   NM_004491   0.79   0.87   0.906709069       GRLF1   NM_004491   0.71   0.80   0.885942625       GTF2B   NM_001514   2.16   2.30   0.937394785       GTF2B   NM_001514   1.95   2.44   0.799673306       GTF2E1   NM_005513   0.76   0.98   0.784112092       GTF2E1   NM_005513   0.74   0.96   0.769972038       GTF2I   NM_001518   2.68   2.80   0.958900201       GTF2I   NM_001518   2.58   2.96   0.869928806       GTF2IP1   AF036613   0.95   0.70   1.359169172       GTF2IP1   AF036613   0.84   0.84   0.988769754       GTF3A   NM_002097   1.49   1.59   0.932083753       GTF3A   NM_002097   1.58   1.70   0.931723008       GTF3C1   NM_001520   2.07   2.25   0.919747554       GTF3C1   NM_001520   1.99   2.34   0.847308047       GTF3C2   NM_001521   1.31   1.28   1.027107124       GTF3C2   NM_001521   1.22   1.29   0.943844023       GTF3C3   NM_012086   1.64   1.64   0.996581398       GTF3C3   NM_012086   1.52   1.67   0.907893639       GTF3C4   NM_012204   1.11   1.28   0.860437792       GTF3C4   NM_012204   1.13   1.33   0.851773956       GTP   AF054183   1.98   2.25   0.880760132       GTP   AF054183   1.86   2.27   0.818437867       H1F3   M60746   1.08   1.27   0.853497342       H1F3   M60746   1.10   1.33   0.824710104       H2AFX   X14850   1.24   1.33   0.934617922       H2AFX   X14850   1.19   1.40   0.849848259       H4   X67081   0.83   0.97   0.859373264       H4   X67081   0.84   1.00   0.842811776       hairless   AF039196   1.39   1.46   0.951801096       hairless   AF039196   1.37   1.53   0.896272718       HAP2   M59079   1.59   1.49   1.062457371       HAP2   M59079   1.33   1.71   0.780793131       HAT1   NM_003642   1.05   0.86   1.223229142       HAT1   NM_003642   1.06   1.04   1.026464835       HB16   M31630   0.97   1.09   0.894291244       HB16   M31630   1.01   1.26   0.797052293       HB9   U07663   2.64   2.61   1.013508831       HB9   U07664   0.92   1.03   0.895489189       HBOA   NM_007067   1.27   1.37   0.929935594       HBOA   NM_007067   1.23   1.35   0.912294782       HCF-2   AF117210   1.43   1.56   0.918694023       HCF-2   AF117210   1.43   1.61   0.888145397       HD-ZNF1   NM_004876   1.11   1.22   0.910541692       HD-ZNF1   NM_004876   1.05   1.19   0.884372648       HDAC1   NM_004964   0.83   0.97   0.851140233       HDAC1   NM_004964   0.82   0.97   0.844737874       HDAC4   NM_006037   2.76   2.40   1.153229661       HDAC4   NM_006037   1.64   1.99   0.825094678       HEB   M83233   0.75   0.89   0.83812814       HEB   M83233   0.73   0.90   0.814864061       HEN1   M96739   1.51   1.61   0.937658625       HEN1   M96739   1.49   1.69   0.883530062       HERP1   AF232238   1.64   1.78   0.918811847       HERP1   AF232238   1.48   1.69   0.873182906       HERP2   AF232239   0.88   0.97   0.913791819       HERP2   AF232239   0.82   1.01   0.814129508       HES4   AB048791   1.12   1.24   0.906421263       HES4   AB048791   1.17   1.31   0.892326717       HGS   NM_004712   1.13   1.22   0.925941974       HGS   NM_004712   1.08   1.23   0.884627755       HIC1   NM_006497   1.01   1.19   0.84718439       HIC1   NM_006497   0.94   1.20   0.789513268       HIVEP1   NM_002114   1.24   1.14   1.08520656       HIVEP1   NM_002114   1.03   1.16   0.893216374       HIVEP2   NM_006734   2.86   2.87   0.99372865       HKE4   NM_006979   1.51   1.70   0.89115193       HKE4   NM_006979   1.35   1.66   0.814320291       HLF   M95585   1.28   1.32   0.971118298       HLF   M95586   1.15   1.26   0.910803018       HMG-1   D63874   1.27   1.25   1.015741343       HMG-1   D63874   1.23   1.22   1.008346304       HMG-2   X62534   1.70   1.82   0.938295788       HMG-2   X62534   1.55   1.76   0.878616998       HMG17   NM_005517   0.99   1.14   0.868604212       HMG17   NM_005517   0.97   1.15   0.841273347       HMGIY   NM_002131   0.92   1.04   0.886466628       HMGIY   NM_002131   0.93   1.13   0.824826257       HNF-1A   M57732   1.03   1.19   0.868596298       HNF-1A   M57732   1.07   1.25   0.861349263       HNF-1B   X71346   2.40   2.21   1.087117438       HNF-1B   X71346   2.25   2.18   1.030922798       HNF-3gamma   L12141   1.46   1.53   0.956635501       HNF-3gamma   L12141   1.40   1.54   0.90844598       HNF-4alpha3   U72967   2.92   3.06   0.953909282       HNF-4alpha3   U72967   2.76   3.16   0.871764387       HNF-6alpha   AF035580   1.20   1.00   1.202677165       HNF-6alpha   AF035580   1.02   1.07   0.954515537       HNF3A   NM_004496   1.35   1.39   0.968770391       HNF3A   NM_004496   1.30   1.39   0.934312714       HOX   L11239   1.29   1.55   0.831459424       HOX   L11239   1.22   1.56   0.784287548       HOX11   s38742   0.82   0.97   0.846268344       HOX11   s38742   0.89   1.06   0.840219605       HOX11L2   AJ223798   5.90   5.44   1.08601856       HOX11L2   AJ223798   5.29   5.47   0.967027069       HOXA-9   U81511   2.28   2.06   1.107860869       HOXA-9   U81511   2.06   2.02   1.019494694       HOXA1   S79910   1.47   1.44   1.023612925       HOXA1   S79910   1.22   1.31   0.930731462       HOXA11   AF071164   1.23   1.36   0.902672948       HOXA11   AF071164   1.28   1.48   0.86247018       HOXA13   NM_000522   7.13   5.19   1.375914112       HOXA13   NM_000522   3.90   4.45   0.876388041       HOXA4   U56105   1.20   1.41   0.854164123       HOXA4   U56105   1.19   1.46   0.814779811       HOXA7   NM_006896   1.14   1.20   0.952764133       HOXA7   NM_006896   1.09   1.21   0.899003953       HOXB1   X16666   1.59   1.81   0.877682176       HOXB1   X16666   1.62   2.00   0.80887332       HOXB2   X78978   1.84   1.60   1.145917       HOXB2   X78978   1.64   1.72   0.957991608       HOXB2   X16665   1.39   1.54   0.905368978       HOXB2   X16665   1.42   1.59   0.895429132       HOXB3   X16667   1.92   1.73   1.107588304       HOXB3   X16667   1.87   1.84   1.015740013       HOXB4   AF005652   1.16   1.27   0.911652213       HOXB4   AF005652   1.09   1.24   0.880915725       HOXB5   M92299   1.18   1.38   0.854344138       HOXB5   M92299   1.20   1.49   0.803737757       HOXB7   M16937   0.95   1.22   0.778800068       HOXB7   M16937   0.97   1.24   0.778387715       HOXC10   AF255675   1.16   1.28   0.905053085       HOXC10   X99685   1.12   1.27   0.881270065       HOXC10   AF255675   1.13   1.31   0.858450467       HOXC10   X99685   1.10   1.33   0.82796661       HOXC6   M16938   1.26   1.49   0.844466889       HOXC6   M16938   1.16   1.46   0.800039127       HOXC8   X99681   1.12   1.30   0.860768554       HOXC8   X99681   0.97   1.24   0.783209726       HOXD3   NM_006898   1.51   1.62   0.92856985       HOXD3   NM_006898   1.47   1.61   0.918716026       HOXD4   X04706   1.24   1.40   0.886519344       HOXD4   X67079   1.56   1.78   0.877418885       HOXD4   X67079   1.54   1.86   0.826005297       HOXD4   X04706   1.22   1.52   0.804048475       HPX42B   NM_014468   1.02   1.04   0.980963071       HPX42B   NM_014468   0.91   1.00   0.913143774       hRev   X72631   1.25   1.35   0.929674185       hRev   X72631   1.28   1.42   0.902255362       HS747E2A   NM_015370   1.07   1.12   0.959032318       HS747E2A   NM_015370   1.02   1.17   0.873166624       HSA275986   NM_018403   1.80   1.66   1.081002809       HSA275986   NM_018403   1.61   1.81   0.888060724       HSBP1   AF068754   2.24   2.62   0.853507954       HSBP1   AF068754   2.27   2.83   0.801085361       HSET   D14678   0.47   0.56   0.84140568       HSET   D14678   0.46   0.59   0.779570541       HSF2BP   NM_007031   2.36   2.61   0.904409562       HSF2BP   NM_007031   2.24   2.57   0.86866997       HSGT1   NM_007265   1.14   1.17   0.973056944       HSGT1   NM_007265   1.12   1.27   0.878498082       hSIM2   D85922   2.71   2.85   0.952407887       hSIM2   D85922   2.65   2.91   0.910509622       Hsp90   X07270   0.92   1.11   0.82588322       Hsp90   X15183   2.01   2.48   0.812100632       hTFIIS.h   AJ223473   0.99   1.13   0.878742961       hTFIIS.h   AJ223473   0.98   1.14   0.856298131       HUNKI   Y12059   1.59   1.62   0.976707993       HUNKI   Y12059   1.33   1.50   0.884627755       HZF2   X78925   1.12   1.19   0.948487222       HZF2   X78925   1.08   1.19   0.908973223       HZF3   X78926   1.28   1.39   0.920945575       HZF3   X78926   1.10   1.31   0.838730175       HZF8   X78931   1.56   1.52   1.022134201       HZF8   X78931   1.40   1.56   0.896953681       HZF9   X78932   1.14   1.24   0.918602524       HZF9   X78932   1.11   1.30   0.857126824       Id1   NM_002165   1.24   1.23   1.00902126       Id1   NM_002165   1.13   1.41   0.80522294       Id3   A17548   1.38   1.31   1.055781754       Id3   X69111   1.27   1.28   0.990641606       Id4   Y07958   1.15   1.26   0.913664616       Id4   Y07958   1.09   1.32   0.830113526       InsAF   s73205   1.84   2.05   0.898920183       InsAF   s73205   1.85   2.13   0.871765981       intergenic region   U15407   2.30   2.60   0.88468389       HOXB7-HOXB6       intergenic region   U15407   2.04   2.59   0.785453268       HOXB7-HOXB6       IQGAP2   NM_006633   1.12   1.12   0.998484582       IQGAP2   NM_006633   0.94   1.12   0.840859025       IRF-1   X14454   2.41   2.57   0.938218115       IRF-1   X14454   2.39   2.58   0.925343204       IRF2   NM_002199   3.34   2.85   1.173965009       IRF2   NM_002199   2.94   2.56   1.14907375       IRF4   U52682   1.32   1.28   1.029933166       IRF4   U52682   1.37   1.43   0.959410817       IRF5   NM_002200   1.37   1.51   0.904052621       IRF5   NM_002200   1.36   1.59   0.858607001       IRF6   NM_006147   1.29   1.58   0.813425333       IRF6   NM_006147   1.18   1.50   0.789190299       IRF7   U53830   1.84   1.44   1.27973546       IRF7   NM_004029   1.32   1.21   1.084000454       Irx-4   NM_016358   1.19   1.15   1.029933166       Irx-4   NM_016358   1.17   1.22   0.956334448       IsGF-3gamma   M87503   1.42   1.55   0.915149715       IsGF-3gamma   M87503   1.39   1.56   0.887975373       Jun-D   X56681   2.38   2.25   1.056280294       Jun-D   X56681   2.04   2.18   0.933938896       JunB   X51345   1.02   1.14   0.892190868       JunB   X51345   0.98   1.14   0.855272625       K-ALPHA-1   NM_006082   0.83   0.96   0.86884485       K-ALPHA-1   NM_006082   0.83   0.97   0.859281424       KF1   NM_005667   0.93   1.05   0.890983333       KF1   NM_005667   0.91   1.06   0.864474263       KIAA0048   D28588   1.17   1.24   0.943988673       KIAA0048   D28588   1.19   1.30   0.918453567       KIAA0065   D31763   2.61   2.47   1.058679492       KIAA0065   D31763   2.53   2.52   1.005681703       KIAA0071   NM_015156   2.49   2.21   1.124047572       KIAA0071   NM_015156   2.30   2.27   1.015956269       KIAA0130   NM_014815   1.35   1.36   0.9886418       KIAA0130   NM_014815   1.17   1.34   0.869733568       KIAA0161   D79983   1.43   1.66   0.85937708       K1AA0161   D79983   1.42   1.69   0.837823111       KIAA0211   D86966   1.41   1.67   0.846204986       KIAA0211   D86966   1.37   1.73   0.79442123       KIAA0222   D86975   2.22   2.40   0.925360475       KIAA0222   D86975   2.02   2.43   0.82835128       KIAA0244   NM_015153   1.54   1.39   1.1095751       KIAA0244   NM_015153   1.45   1.36   1.067040755       KIAA0314   AB002312   2.38   2.57   0.927343337       KIAA0314   AB002312   2.33   2.65   0.876030662       KIAA0333   AB002331   1.05   1.22   0.861487483       KIAA0333   AB002331   1.07   1.25   0.854015656       KIAA0352   NM_014830   2.88   3.18   0.9057295       KIAA0352   NM_014830   2.37   2.80   0.8492877       KIAA0395   AB007855   1.56   1.77   0.879373168       KIAA0395   AB007855   1.42   1.77   0.801179995       KIAA0426   NM_014724   1.17   1.17   0.995781911       KIAA0426   NM_014724   1.06   1.23   0.866553199       KIAA0478   AB007947   2.27   2.38   0.954072874       KIAA0478   AB007947   2.25   2.62   0.857934327       KIAA0569   NM_014795   1.66   1.65   1.011174941       KIAA0569   NM_014795   1.39   1.76   0.78836631       KIAA0595   AB011167   1.90   1.85   1.026787356       KIAA0595   AB011167   1.71   2.19   0.782500333       KIAA0600   AB011172   1.90   1.34   1.413460448       KIAA0600   AB011172   2.18   1.58   1.381300612       KIAA0929   AB023146   1.54   1.62   0.949493335       KIAA0929   AB023146   1.55   1.63   0.949132006       KIAA1015   AB023232   2.58   2.62   0.982939758       KIAA1015   AB023232   2.17   2.68   0.811021231       KIAA1259   AB033085   0.85   1.04   0.817749165       KIAA1259   AB033085   0.91   1.18   0.771007682       KIAA1442   AB037863   2.14   2.34   0.914709549       KIAA1442   AB037863   2.15   2.39   0.898110711       KIAA1528   AB040961   6.42   6.40   1.003589265       KIAA1528   AB040961   6.67   6.98   0.955545485       KIAA1741   AW081989   1.58   1.79   0.882769399       KIAA1741   AW081989   1.68   1.99   0.846731464       KID   D38751   1.54   1.48   1.042612741       KID   D38751   1.45   1.52   0.95955196       KLF13   NM_015995   1.04   1.28   0.816419879       KLF13   NM_015995   0.91   1.14   0.796485569       KNSL4   AB017335   1.22   1.41   0.866676983       KNSL4   AB017335   1.19   1.45   0.818446687       Kox1   X52332   1.02   1.16   0.880125266       Kox1   X52332   0.98   1.24   0.789133958       Kox23   X52354   0.91   1.08   0.842330108       Kox23   X52354   0.90   1.08   0.832659332       Kox26   X52357   1.00   1.19   0.83622347       Kox26   X52357   0.99   1.26   0.785398373       Kox29   X52360   0.96   1.07   0.90087877       Kox29   X52360   0.98   1.09   0.897521031       Kox30   X52361   1.58   1.72   0.918425379       Kox30   X52361   1.38   1.53   0.902401118       KRAB   M67508   1.56   1.63   0.955633904       KRAB   M67508   1.47   1.60   0.922478172       Kruppel-type ZNF   AJ245587   2.04   2.40   0.851750841       Kruppel-type ZNF   AJ245587   1.79   2.14   0.836843037       KUP   X16576   0.96   1.15   0.839112982       KUP   X16576   0.92   1.13   0.816714046       L-Myc-1(long form)   X07262   1.05   1.20   0.876584744       L-Myc-1(long form)   X07262   1.01   1.23   0.826416004       LAF4   NM_002285   0.67   0.83   0.815483937       LAF4   NM_002285   0.65   0.84   0.784014372       LBR   NM_002296   1.25   1.30   0.966371608       LBR   NM_002296   1.23   1.38   0.891519857       LD5-1   U88080   1.15   1.38   0.82971758       LD5-1   U88080   1.11   1.41   0.790825308       LDOC1   NM_012317   1.33   1.41   0.946393907       LDOC1   NM_012317   1.28   1.42   0.897325005       LEF-1   AF203908   1.27   1.37   0.928294795       LEF-1   AF203908   1.16   1.44   0.810978586       lens epithelium-derived   AF063020   1.24   1.42   0.870186854       GF       lens epithelium-derived   AF063020   1.13   1.39   0.81400662       GF       leucine zipper   AF056184   2.24   2.72   0.824441293       leucine zipper   AF056184   2.47   3.10   0.796652442       leucine zipper kinase   AF251441   2.80   3.31   0.846204986       AZK       leucine zipper kinase   AF251441   2.71   3.35   0.808081689       AZK       LHX2   NM_004789   1.42   1.48   0.953866869       LHX2   NM_004789   1.33   1.52   0.87550605       LHX6   NM_014368   1.31   1.42   0.921284172       LHX6   NM_014368   1.28   1.42   0.905610681       LIM   AF061258   1.13   1.44   0.78655152       LIM   AF061258   1.09   1.41   0.773071315       LIM domain only 1   M26682   1.39   1.44   0.966564434       (rhombotin 1)       LIM domain only 1   M26682   1.32   1.49   0.883805842       (rhombotin 1)       LIM protein MLP   U49837   0.96   1.03   0.937706079       LIM protein MLP   U49837   0.95   1.14   0.82868354       LIM1   U14755   1.17   1.23   0.952256263       LIM1   U14755   1.01   1.27   0.798369687       LIMK   D26309   2.92   3.03   0.964180024       LIMK-2   D45906   1.60   1.66   0.965944664       LIMK-2   D45906   1.63   1.73   0.945399728       LMO4   U24576   0.85   0.84   1.007125772       LMO4   U24576   0.85   0.88   0.960803963       LOC51043   NM_015872   0.86   0.91   0.949928525       LOC51043   NM_015872   0.96   1.02   0.943797482       LOC51131   NM_016119   1.08   1.04   1.041898041       LOC51131   NM_016119   1.01   1.03   0.974830053       LOC51193   NM_016331   1.18   1.40   0.846337164       LOC51193   NM_016331   1.26   1.54   0.817829826       LOC51591   NM_015905   5.44   4.01   1.354983586       LOC51591   NM_015905   5.77   4.26   1.353823958       LOC51717   NM_016285   1.43   1.55   0.919576048       LOC51717   NM_016285   1.32   1.54   0.856030646       LOC55862   NM_018479   3.18   3.29   0.96566812       LOC55862   NM_018479   2.90   3.29   0.882904561       LOC56899   AF164792   1.35   1.46   0.923685155       LOC56899   AF164792   1.24   1.47   0.843151755       LyF-1   U40462   1.17   1.33   0.881798663       LyF-1   U40462   1.04   1.28   0.809448886       LZLP   NM_013344   1.63   1.78   0.914937922       LZLP   NM_013344   1.50   1.67   0.897409878       MADH4   NM_005359   1.48   1.23   1.202041185       MADH4   NM_005359   1.27   1.13   1.118588098       MADH5   NM_005903   1.19   1.37   0.867598314       MADH5   NM_005903   1.20   1.38   0.864484722       MAF   NM_005360   0.82   0.83   0.983383327       MAF   NM_005360   0.74   0.92   0.79706277       MAFG   NM_002359   1.33   1.60   0.833961234       MAFG   NM_002359   1.37   1.65   0.833526497       MAP4   NM_002375   3.80   4.62   0.824293011       MAP4   NM_002375   3.69   4.71   0.78417244       MAPK8   NM_002750   0.88   1.00   0.88152506       MAPK8   NM_002750   0.88   1.02   0.860049569       MAZ   M94046   1.21   1.47   0.819442731       MAZ   M94046   1.19   1.48   0.804052549       MB67   Z30425   1.08   1.02   1.060408157       MB67   Z30425   0.99   1.08   0.915952791       MCG4   NM_006782   1.15   1.31   0.87362439       MCG4   NM_006782   1.15   1.34   0.857557298       MEF2A   U49020   1.18   1.29   0.917750293       MEF2A   U49020   1.08   1.27   0.851735738       MEF2B   NM_005919   1.02   1.07   0.950137026       MEF2B   NM_005919   0.95   1.04   0.910069513       MEF2D   NM_005920   1.39   1.33   1.043108425       MEF2D   NM_005920   1.20   1.44   0.837034123       metallopanstimulin   U85979   1.98   2.01   0.985678226       metallopanstimulin   U85979   1.94   2.20   0.882570172       MHox (K-2)   M95929   1.07   1.17   0.914292266       MHox (K-2)   M95929   0.95   1.17   0.810474232       Mi   Z29678   1.71   1.66   1.030471845       Mi   Z29678   1.76   1.79   0.986205176       MITF   AF034755   1.23   1.24   0.99130983       MITF   AF034755   1.32   1.50   0.883057308       Miz-1   Y09723   1.01   1.15   0.876000186       Miz-1   Y09723   0.93   1.14   0.814161592       MLH3   NM_005784   0.54   0.63   0.855999025       MLH3   NM_005784   0.62   0.78   0.801334083       MLX   AF203978   1.41   1.49   0.949042398       MLX   AF203978   1.36   1.48   0.923306997       Mog   U64564   1.32   1.37   0.960484338       Mog   U64564   1.27   1.39   0.915925265       MRG1   AF109161   3.76   4.37   0.860312626       MRG1   AF109161   3.73   4.50   0.827783082       MTERF   NM_006980   1.51   1.80   0.838119573       MTERF   NM_006980   1.35   1.70   0.789625228       MTF-1   AJ251881   2.11   2.39   0.881959401       MTF-1   AJ251881   1.95   2.39   0.815353763       mtTF1   X64269   1.47   1.59   0.925536704       mtTF1   X64269   1.44   1.57   0.914838473       MXI1   NM_005962   1.16   1.29   0.898657286       MXI1   NM_005962   1.16   1.36   0.857867078       MYBBP1A   AF147709   2.29   1.77   1.292847997       MYBBP1A   AF147709   1.85   1.75   1.054649057       MYCBP   NM_012333   3.73   3.58   1.040887845       MYCBP   NM_012333   3.47   3.48   0.997884909       MYCL2   NM_005377   2.12   2.03   1.044677307       MYCL2   NM_005377   2.04   2.00   1.018897998       MYCLK1   M64786   1.43   1.73   0.828883125       MYCLK1   M64786   1.49   1.80   0.826354974       MYT2   NM_003871   4.01   4.17   0.962205771       MYT2   NM_003871   4.04   4.42   0.915182881       N-CoR   AF044209   1.33   1.29   1.027153581       N-CoR   AF044209   1.25   1.29   0.969389141       N-Oct-3   Z11933   3.50   3.17   1.103689021       N-Oct-3   Z11933   2.91   3.05   0.955346496       N143   AJ002572   3.89   3.16   1.232431216       N143   AJ002572   2.82   3.41   0.828068155       NACA   NM_005594   1.34   1.26   1.061449635       NACA   NM_005594   1.22   1.36   0.899257451       NAGA   NM_000262   2.23   2.55   0.873072079       NAGA   NM_000262   2.02   2.54   0.795967326       NCOA1   NM_003743   1.34   1.43   0.939022342       NCOA1   NM_003743   1.36   1.45   0.932646647       NCOA3   NM_006534   2.14   2.15   0.995002762       NCOA3   NM_006534   1.97   2.05   0.959254041       NCYM   NM_006316   1.18   1.11   1.067219564       NCYM   NM_006316   1.07   1.16   0.917384574       NDUFA6   NM_002490   0.80   0.82   0.969899497       NDUFA6   NM_002490   0.71   0.92   0.772339515       Negative control   Negative control   1.29   1.11   1.161392449       Negative control   Negative control   5.43   5.29   1.027043989       NEUROD2   U58681   1.14   1.28   0.889551897       NEUROD2   U58681   1.02   1.28   0.795592113       NEUROG1   U63842   1.39   1.71   0.812574039       NEUROG1   U63842   1.29   1.63   0.795487149       NF-1X   U07811   0.99   0.82   1.215806558       NF-1X   U07811   0.64   0.82   0.782275487       NFAT1   U43341   2.28   2.65   0.861852199       NFAT1   U43341   2.30   2.80   0.819721245       NFATC1   NM_006162   1.21   1.27   0.956885723       NFATC1   NM_006162   1.20   1.33   0.906442678       NFATX   U14510   1.09   1.35   0.8066644       NFATX   U14510   0.99   1.24   0.798995238       NFIL3   NM_005384   3.33   3.43   0.969982487       NFIL3   NM_005384   3.22   3.36   0.957589194       NFKB1   M58603   2.44   2.68   0.910234175       NFKB1   M55643   1.23   1.37   0.894069494       NFKB2   U09609   1.09   1.21   0.899003953       NFKB2   U09609   1.04   1.28   0.815426014       NFKBIB   NM_002503   0.66   0.74   0.891632657       NFKBIB   NM_002503   0.61   0.73   0.835589511       NFKBIE   NM_004556   1.34   1.34   0.995844935       NFKBIE   NM_004556   1.30   1.37   0.951450999       NFkBp105   M55643   0.82   0.80   1.028950235       NFkBp105   M55643   0.78   0.88   0.882630106       ngn3   AJ133776   1.04   1.14   0.911675496       ngn3   AJ133776   1.01   1.15   0.877939013       NME2   NM_002512   1.08   1.28   0.849242645       NME2   NM_002512   0.99   1.21   0.819907039       Nmi   U32849   1.50   1.65   0.908824603       Nmi   U32849   1.46   1.67   0.874987469       NOD1   AF149774   0.88   0.97   0.913819737       NOD1   AF149774   0.80   0.97   0.829329103       NOT3   NM_014516   1.10   1.05   1.043010425       NOT3   NM_014516   1.01   1.32   0.770565768       NP220   D83032   1.59   1.80   0.886060234       NP220   D83032   1.50   1.74   0.861556367       NPAS1   NM_002517   2.55   3.06   0.832115639       NPAS1   NM_002517   2.53   3.18   0.795687598       NR0B1   NM_000475   0.89   0.90   0.985394227       NR0B1   NM_000475   0.84   1.02   0.822398708       NR2F6   NM_005234   1.11   1.26   0.878406569       NR2F6   NM_005234   1.03   1.23   0.843593242       NR3C1   NM_000176   1.45   1.63   0.884627755       NR3C1   NM_000176   1.37   1.57   0.872392013       NR4A2   NM_006186   5.15   5.52   0.933470433       NR4A2   NM_006186   4.88   5.68   0.859257687       NR5A1   NM_004959   1.55   1.88   0.827098402       NR5A1   NM_004959   1.56   1.94   0.806250074       NRL   M81840   1.12   1.36   0.824507422       NRL   M81840   1.08   1.34   0.802675923       NRsF form 2   U13879   1.51   1.60   0.940689035       NRsF form 2   U13879   1.29   1.56   0.826356612       NSEP1   NM_004559   4.08   4.54   0.898882683       NSEP1   NM_004559   4.09   4.85   0.843016697       nuclear factor 1 B-type   U07810   1.67   1.72   0.970651102       nuclear factor 1 B-type   U07810   1.50   1.56   0.957498055       nuclear factor I-B2   U85193   5.86   6.80   0.86191166       nuclear factor I-B2   U85193   6.04   7.09   0.85215085       nuclear factor IV   X57500   1.44   1.28   1.118113871       nuclear factor IV   X57500   1.35   1.53   0.882482444       OAZ   AF221712   0.95   0.98   0.974744849       OAZ   AF221712   0.82   0.94   0.867200363       Oct-1B = POU   S66902   1.11   1.23   0.901795827       homeodomain       Oct-1B = POU   S66902   1.07   1.22   0.879755632       homeodomain       Oct-4A   Z11900   1.44   1.75   0.825538314       Oct-4A   Z11900   1.43   1.85   0.773109431       OGL12   AF023203   2.31   2.68   0.864811744       OGL12   AF023203   2.45   2.92   0.837215348       OSMRB   U60805   0.90   1.09   0.825581       OSMRB   U60805   0.78   0.97   0.805457565       OTF3C   Z11901   6.19   4.42   1.40097838       OTF3C   Z11901   5.89   4.42   1.332945525       OTX1   AB037501   1.87   1.84   1.018457389       OTX1   AB037501   1.75   1.86   0.938379       OVOL1   NM_004561   1.34   1.20   1.12018921       OVOL1   NM_004561   1.05   1.21   0.869990813       p130   s67171   2.11   1.71   1.231079229       p130   s67171   1.56   1.60   0.975948711       p243   AJ242977   1.27   1.43   0.884227005       p243   AJ242977   1.37   1.69   0.812266478       P38IP   NM_017569   0.99   1.09   0.90720651       P38IP   NM_017569   0.94   1.10   0.856087428       p53   K03199   1.39   1.68   0.831158406       p53   K03199   1.38   1.67   0.828166161       p621   AJ242978   1.19   1.20   0.990516633       p621   AJ242978   1.06   1.18   0.898178687       PACE4   NM_002570   1.29   1.48   0.867988727       PACE4   NM_002570   1.26   1.48   0.852795758       PAX1   NM_006192   1.20   1.32   0.903818349       PAX1   NM_006192   1.06   1.32   0.807894213       PAX2   U45255   1.46   1.62   0.901165711       PAX2   U45255   1.40   1.63   0.858751434       PAX3   NM_000438   1.21   1.36   0.886358667       PAX3   NM_000438   1.16   1.37   0.850478749       PAX5   U56835   0.93   1.06   0.871188843       PAX5   NM_016734   1.71   2.02   0.846266       PAX6   U63833   1.33   1.53   0.865756264       PAX6   U63833   1.27   1.52   0.833925287       PAX8   S55490   1.94   2.07   0.934433059       PAX8   S55490   1.82   2.05   0.885815601       PAX9   NM_006194   0.78   0.95   0.817959194       PAX9   X92850   1.17   1.49   0.784900153       PBX1   NM_002585   1.46   1.26   1.160624187       PBX1   NM_002585   1.56   1.36   1.14486291       PBX2   NM_002586   1.14   1.28   0.885932245       PBX2   NM_002586   1.14   1.34   0.848773413       PC4   NM_006713   0.70   0.80   0.879994421       PC4   NM_006713   0.70   0.81   0.86301099       PCAF   NM_003884   1.07   1.34   0.798415415       PCAF   NM_003884   1.03   1.29   0.796481403       PDEF   NM_012391   1.17   1.33   0.876561702       PDEF   NM_012391   1.38   1.70   0.811137032       PEA3   D12765   1.21   1.54   0.784602478       PEA3   D12765   1.21   1.56   0.775569587       PEPD   J04605   0.66   0.78   0.8570049       PEPD   J04605   0.71   0.86   0.827558815       PGF   NM_002632   1.08   1.18   0.917061973       PGF   NM_002632   1.01   1.20   0.83593402       pGLI3HH   M20674   1.21   1.31   0.921799298       pGLI3HH   M20674   1.13   1.32   0.856812924       PIAS3   NM_006099   3.47   4.09   0.849170482       PIAS3   NM_006099   3.59   4.26   0.842175439       PINCH   U09284   1.62   1.49   1.088214315       PINCH   U09284   1.44   1.44   1.001116263       Pit-1   D10216   2.56   2.74   0.934572932       Pit-1   D10216   2.26   2.72   0.831778211       PITX1   NM_002653   1.04   1.23   0.841903944       PITX1   NM_002653   0.95   1.22   0.780247958       PITX2   U69961   2.17   1.90   1.142972468       PITX2   U69961   1.90   1.73   1.099447256       PITX3   NM_005029   1.08   1.19   0.908904038       PITX3   NM_005029   1.05   1.16   0.900257494       PKNOX1   NM_004571   2.66   2.91   0.915727678       PKNOX1   NM_004571   2.43   2.80   0.867326045       PLCG1   NM_002660   0.88   1.09   0.801330479       PLCG1   NM_002660   0.87   1.12   0.777390419       PML   M79462   2.93   3.22   0.90918611       PML   M79462   2.83   3.18   0.891376967       POU6F1   NM_002702   1.18   1.38   0.853348217       POU6F1   NM_002702   1.11   1.39   0.803725887       PPAR delta   AF187850   1.68   2.05   0.817974153       PPAR delta   AF187850   1.63   2.05   0.797208472       PPARbeta   L07592   1.12   1.30   0.860735779       PPARbeta   L07592   1.09   1.30   0.841097109       PPARBP   NM_004774   2.49   2.42   1.028888699       PPARBP   NM_004774   2.59   2.62   0.989587372       PPARG   NM_005037   1.76   1.92   0.919451555       PPARG   NM_005037   1.54   1.87   0.82431469       PPARGC1   NM_013261   4.02   4.08   0.985608174       PPARGC1   NM_013261   3.61   3.97   0.910308604       PPIH   NM_006347   1.11   1.36   0.810066673       PPIH   NM_006347   1.10   1.37   0.797849135       pRb   X16439   1.29   1.40   0.923240454       pRb   X16439   1.21   1.44   0.839720657       PRDM4   NM_012406   1.09   1.14   0.952491603       PRDM4   NM_012406   1.02   1.09   0.935085892       protein Id4   U28368   1.18   1.11   1.06450375       protein Id4   U28368   1.29   1.23   1.054319434       protein p38   AJ242975   1.63   1.95   0.834950074       protein p38   AJ242975   1.44   1.85   0.781801717       PRX2   NM_016307   4.82   3.63   1.326456916       PRX2   NM_016307   4.32   4.25   1.017671923       PSCDBP   NM_004288   0.74   0.85   0.86992699       PSCDBP   NM_004288   0.69   0.84   0.81936229       PSMC1   NM_002802   1.36   1.52   0.894759062       PSMC1   NM_002802   1.18   1.33   0.891456342       PTHR1   NM_000316   1.31   1.42   0.924499528       PTHR1   NM_000316   1.20   1.40   0.8556512       PXMP3   NM_000318   1.62   2.02   0.804068402       PXMP3   NM_000318   1.40   1.80   0.78066981       PXN   NM_002859   2.72   2.90   0.93925013       PXN   NM_002859   2.51   2.90   0.863012935       rab 13   X75593   1.25   1.23   1.008775651       rab 13   X75593   1.12   1.33   0.83974611       RAR-alpha1   X06614   1.43   1.62   0.88166305       RAR-alpha1   X06614   1.30   1.60   0.814209521       RAR-b   M96016   1.57   1.95   0.801619789       RAR-b   M96016   1.57   2.00   0.782949951       RARA   NM_000964   1.42   1.65   0.862685131       RARA   NM_000964   1.40   1.65   0.847918555       RARG   NM_000966   1.42   1.61   0.882296859       RARG   NM_000966   1.41   1.60   0.882261145       RB1   NM_000321   0.97   1.19   0.812728745       RB1   NM_000321   0.96   1.20   0.800478062       RBL1   NM_002895   2.04   2.42   0.841470759       RBL1   NM_002895   1.92   2.35   0.817621225       RBP-L   AB026048   0.94   0.70   1.339824561       RBP-L   AB026048   0.80   0.71   1.133824475       RCL   NM_006443   1.26   1.39   0.906711617       RCL   NM_006443   1.24   1.39   0.891529469       RELA   Z22951   0.86   0.89   0.96567493       RELA   Z22951   0.80   0.85   0.94852389       repressor protein   D30612   1.37   1.53   0.890929984       repressor protein   D30612   1.32   1.52   0.87316143       REQ   NM_006268   1.43   1.67   0.860238236       REQ   NM_006268   1.46   1.72   0.847602428       retinoid X receptor   U66306   2.17   2.44   0.889382828       alpha       retinoid X receptor-   U38480   2.07   2.33   0.889199662       gamma       RFP   NM_006510   3.73   3.97   0.940382915       RFP   NM_006510   3.81   4.43   0.858648769       RFX3   X76092   1.62   1.47   1.1024024       RFX3   X76092   1.43   1.62   0.8816817       rhoHP1   D85815   1.42   1.33   1.069393174       rhoHP1   D85815   1.46   1.53   0.955107329       RING1   NM_002931   1.42   1.59   0.896164283       RING1   NM_002931   1.41   1.60   0.880810591       RLF   NM_012421   3.38   3.75   0.901013305       RLF   NM_012421   3.65   4.07   0.898102049       RNF NY-REN-43   AF155109   1.18   1.29   0.913146151       RNF NY-REN-43   AF155109   1.16   1.43   0.811644103       RNF13   NM_007282   1.22   1.33   0.916119358       RNF13   NM_007282   1.20   1.31   0.912867135       RNF15   NM_006355   1.29   1.45   0.893216374       RNF15   NM_006355   1.17   1.44   0.811128245       RNF4   NM_002938   1.35   1.44   0.936370857       RNF4   NM_002938   1.32   1.45   0.907740218       RNF9   NM_006778   1.25   1.36   0.918123369       RNF9   NM_006778   1.18   1.36   0.863185084       RNP-specific A   X06347   1.31   1.39   0.94551044       RNP-specific A   X06347   1.16   1.47   0.788038353       RORalpha2   U04898   4.15   4.42   0.938764319       RORalpha2   U04898   4.03   4.29   0.938708029       RORbeta   Y08639   1.29   1.50   0.858111801       RORbeta   Y08639   1.27   1.50   0.842642276       RORC   NM_005060   1.39   1.61   0.861315789       RORC   NM_005060   1.43   1.77   0.807520338       RP58   AJ223321   1.34   1.40   0.953320654       RP58   AJ223321   1.19   1.38   0.866072097       RPF-1   U91934   1.26   1.51   0.833565324       RPF-1   U91934   1.23   1.50   0.822227125       RPL13A   X56932   0.87   0.88   0.991870123       RPL13A   X56932   0.77   0.87   0.883814097       RPL15   NM_002948   1.01   1.07   0.944600915       RPL15   NM_002948   0.98   1.14   0.859452181       RPL21   NM_000982   1.60   1.53   1.04809166       RPL21   NM_000982   1.57   1.58   0.995425213       RPL23A   NM_000984   1.59   1.42   1.117137899       RPL23A   NM_000984   1.46   1.38   1.059317332       RPL37   NM_000997   1.09   1.23   0.883744302       RPL37   NM_000997   1.09   1.30   0.842639916       RPS11   NM_001015   1.55   1.32   1.171184602       RPS11   NM_001015   1.30   1.22   1.068789518       RPS19   NM_001022   0.84   1.00   0.841774594       RPS19   NM_001022   0.86   1.05   0.819892642       RRN3   NM_018427   1.64   1.61   1.015843155       RRN3   NM_018427   1.10   1.40   0.78552954       RUVBL1   NM_003707   1.21   1.41   0.864080705       RUVBL1   NM_003707   1.15   1.43   0.805614035       Rx   AF001911   1.40   1.19   1.169408279       Rx   AF001911   1.21   1.29   0.940515001       RXR-alpha   X52773   1.14   1.20   0.95178794       RXR-alpha   X52773   1.02   1.17   0.875212013       RXRB   U00961   1.41   1.76   0.802764083       RXRB   U00961   1.32   1.64   0.802187954       SAFB   NM_002967   2.08   1.85   1.122521568       SAFB   NM_002967   1.98   1.85   1.072239203       SALL1   NM_002968   1.06   1.32   0.799379966       SALL1   NM_002968   1.09   1.37   0.794919835       sAP-1a   M85165   1.02   1.15   0.893216374       sAP-1a   M85165   0.99   1.14   0.868660598       SEP3B   AF285109   1.36   1.52   0.895524427       SEP3B   AF285109   1.34   1.51   0.891662954       sF1   D88155   1.24   1.23   1.006655807       sF1   D88155   0.89   1.10   0.815406356       SF3A1   NM_005877   0.94   1.18   0.796947498       SF3A1   NM_005877   0.98   1.24   0.789354005       SIX1   X91868   1.28   1.26   1.011940877       SIX1   X91868   1.15   1.27   0.899649002       SIX6   AF141651   1.31   1.51   0.866808238       SIX6   AF141651   1.28   1.61   0.795100662       SKI   NM_003036   1.27   1.34   0.951830965       SKI   NM_003036   1.23   1.34   0.916814067       SKIL   NM_005414   1.22   1.23   0.996060051       SKIL   NM_005414   1.18   1.23   0.965665088       Smad2   U78726   1.54   1.70   0.902843033       Smad2   U78726   1.52   1.74   0.876401307       SMARCA3   NM_003071   2.60   2.63   0.988267744       SMARCA3   NM_003071   2.52   2.58   0.977550509       SMARCA4   NM_003072   1.20   1.41   0.850958457       SMARCA4   NM_003072   1.14   1.43   0.798506046       SMARCC1   NM_003074   1.37   1.53   0.897049921       SMARCC1   NM_003074   1.31   1.51   0.867695906       SMARCC2   NM_003075   1.11   1.36   0.816630385       SMARCC2   NM_003075   1.10   1.37   0.803295263       SMN1   U18423   2.14   2.06   1.0410434       SMN1   U18423   1.93   2.06   0.938075938       SNAP190   AF032387   1.08   1.15   0.940066948       SNAP190   AF032387   1.19   1.34   0.88972042       SNAPC3   NM_003084   0.64   0.65   0.973605848       SNAPC3   NM_003084   0.58   0.67   0.873988625       snRNP B   X17567   0.99   0.98   1.010085806       snRNP B   X17567   0.82   0.97   0.840177885       SOX10   AJ001183   1.71   1.82   0.937524016       SOX10   AJ001183   1.59   1.78   0.894532832       SOX13   NM_005686   1.71   1.92   0.891384762       SOX13   NM_005686   1.66   1.93   0.860515571       SOX4   X70683   0.90   0.93   0.960960313       SOX4   X70683   0.82   0.92   0.894488762       SOX6   X65663   0.69   0.79   0.882795517       SOX6   X65663   0.65   0.75   0.87280897       SOX8   AF164104   1.79   2.09   0.857375717       SOX8   AF164104   1.65   2.13   0.774778844       SOX9   Z46629   1.69   1.88   0.898185589       SOX9   Z46629   1.55   1.92   0.807916038       SP1   J03133   1.18   1.30   0.909375062       SP1   J03133   1.16   1.30   0.887824726       SP3   X68560   1.66   1.66   1.001079125       SP3   X68560   1.45   1.77   0.818395433       sRF   J03161   1.45   1.67   0.867315899       sRF   J03161   1.43   1.69   0.84824421       sRY   L10101   1.18   1.21   0.982441028       sRY   L10101   1.13   1.21   0.934783803       STAT2   M97934   1.41   1.52   0.926980567       STAT2   M97934   1.41   1.62   0.868724958       STAT5B   NM_012448   1.56   1.40   1.114847778       STAT5B   NM_012448   1.40   1.71   0.821978259       STAT6   NM_003153   1.27   1.36   0.938049629       STAT6   NM_003153   1.21   1.37   0.879605458       SZF1   NM_016089   1.21   1.50   0.802961061       SZF1   NM_016089   1.16   1.49   0.774800507       T-STAR   NM_006558   0.67   0.78   0.861849244       T-STAR   NM_006558   0.68   0.82   0.831664605       T3R   Y00479   1.71   1.62   1.053389262       T3R   Y00479   1.60   1.53   1.041322337       T3R   X55066   1.56   1.89   0.824459774       TAF(I)63   L39061   1.00   1.12   0.896350467       TAF(I)63   L39061   1.02   1.30   0.783696377       TAF(II)30   U25816   1.51   1.40   1.074026032       TAF(II)30   U25816   1.40   1.38   1.015134059       TAF(II)32   U21858   0.98   1.22   0.802461769       TAF(II)32   U21858   0.98   1.23   0.792812413       TAF(II)70-alpha   L25444   0.96   1.02   0.941312641       TAF(II)70-alpha   L25444   0.90   1.03   0.872787029       TAF2A   NM_004606   1.13   1.14   0.999330892       TAF2A   NM_004606   0.93   1.11   0.838249213       TAF2F   NM_005642   1.03   1.26   0.81530342       TAF2F   NM_005642   1.02   1.30   0.784947723       TAF2I   NM_005643   1.50   1.43   1.045218429       TAF2I   NM_005643   1.39   1.41   0.991353741       TAF2I   AF118094   1.11   1.26   0.881120736       TAF2J   NM_005644   1.28   1.40   0.913232427       TAF2J   NM_005644   1.23   1.45   0.849684168       TAF2K   NM_005645   2.39   2.40   0.997067405       TAF2K   NM_005645   2.40   2.47   0.972697492       TAFII105   Y09321   1.26   1.45   0.867396208       TAFII105   Y09321   1.19   1.45   0.818176516       Tal-1   NM_003189   1.37   1.51   0.902488517       Tal-1   NM_003189   1.27   1.53   0.828923165       TARBP2   NM_004178   1.09   1.24   0.873471591       TARBP2   NM_004178   1.08   1.37   0.786576406       TBP   NM_003194   2.77   2.67   1.040623399       TBP   NM_003194   2.51   2.58   0.973841382       TBPL1   NM_004865   1.28   1.30   0.987855849       TBPL1   NM_004865   1.11   1.40   0.794804113       TBR1   NM_006593   1.19   1.20   0.996692807       TBR1   NM_006593   1.05   1.26   0.836636729       TBX19   NM_005149   1.36   1.48   0.923280344       TBX19   NM_005149   1.44   1.59   0.909429873       TBX2   NM_005994   0.85   1.07   0.798962867       TBX2   NM_005994   0.83   1.06   0.785853316       TBX20   AJ237589   1.34   1.21   1.102533818       TBX20   AJ237589   1.36   1.64   0.831910222       TBX6   NM_004608   4.15   4.62   0.899551242       TBX6   NM_004608   3.96   4.53   0.875140298       TCEA1   NM_006756   1.27   1.14   1.110125734       TCEA1   NM_006756   1.16   1.11   1.05196336       TCEB2   NM_007108   0.58   0.43   1.337134151       TCEB2   NM_007108   0.51   0.40   1.277713489       TCF-1   Z47365   1.00   1.16   0.86404602       TCF-1   Z47365   0.92   1.18   0.774647829       TCF-4   Y11306   1.36   1.46   0.928464375       TCF-4   Y11306   1.32   1.56   0.849608167       TCF21   NM_003206   1.75   2.02   0.863693344       TCF21   NM_003206   1.69   2.12   0.798699048       TCF4   NM_003199   0.93   0.92   1.021001263       TCF4   NM_003199   0.84   0.92   0.912194059       TCF6L1   NM_003201   1.67   1.95   0.857799865       TCF6L1   NM_003201   1.82   2.34   0.776883554       TCFL1   NM_005997   1.45   1.63   0.891060583       TCFL1   NM_005997   1.45   1.68   0.863907712       TCFL5   NM_006602   1.87   2.31   0.809256058       TCFL5   NM_006602   1.79   2.27   0.788010751       TEAD1   M63896   1.97   2.40   0.821174945       TEAD1   M63896   1.84   2.35   0.783305005       TEF-4   X94440   1.14   1.29   0.883210896       TEF-4   X94440   1.13   1.33   0.854457478       TF   U79243   1.42   1.54   0.919800195       TF   U79243   1.29   1.63   0.789904601       TFCP2   NM_005653   0.99   1.11   0.887949768       TFCP2   NM_005653   0.94   1.13   0.832221275       TFE3   AL161985   1.20   1.25   0.952888449       TFE3   AL161985   1.16   1.30   0.896818053       TFIIA   NM_015859   0.84   0.82   1.018380452       TFIIA   NM_015859   0.80   0.82   0.977671128       TFIID   Z22828   2.50   2.34   1.068758898       TFIID   Z22828   2.55   2.73   0.936976254       TFIIH-cyclin H   U11791   1.28   0.95   1.34843684       TFIIH-cyclin H   U11791   1.29   0.98   1.318842969       TFIIH-MO15   X77743   2.43   2.39   1.014330459       TFIIH-MO15   X77743   2.43   2.39   1.012865369       TFIIH-p34   Z30093   2.74   2.96   0.92722107       TFIIH-p34   Z30093   2.34   2.95   0.792209645       TFRC   NM_003234   1.33   1.49   0.895571075       TFRC   NM_003234   1.28   1.59   0.809200973       TGIF   NM_003244   1.75   1.38   1.274809288       TGIF   NM_003244   1.52   1.51   1.004868421       TIEG2   NM_003597   1.39   1.48   0.938352308       TIEG2   NM_003597   1.35   1.51   0.889349637       TIF1GAMMA   NM_015906   1.01   1.27   0.800846532       TIF1GAMMA   NM_015906   1.01   1.30   0.777179202       TIF2   X97674   1.33   1.45   0.922316636       TIF2   X97674   1.31   1.45   0.902108121       TIM44   NM_006351   1.33   1.57   0.847735407       TIM44   NM_006351   1.36   1.61   0.84323103       Timeless   AF098162   2.00   2.39   0.833636058       Timeless   AF098162   1.93   2.42   0.796169622       TIMM8b   AF152350   1.40   1.42   0.984849477       TIMM8b   AF152350   1.42   1.51   0.941288783       TIMM9   NM_012460   0.71   0.77   0.920513309       TIMM9   NM_012460   0.68   0.84   0.805700618       Tis11d   U07802   1.12   1.35   0.827564107       Tis11d   U07802   1.04   1.27   0.821167897       TNRC11   NM_005120   0.88   1.05   0.836486567       TNRC11   NM_005120   0.85   1.05   0.802230359       TOB1   NM_005749   1.02   1.29   0.790953507       TOB1   NM_005749   1.02   1.32   0.77856472       TOP1   U07806   3.49   3.40   1.026563028       TOP1   U07806   3.18   3.15   1.008577791       TP53BP1   NM_005657   0.83   0.86   0.969466553       TP53BP1   NM_005657   0.79   0.86   0.910836728       TP73   NM_005427   4.36   4.73   0.923146915       TP73   NM_005427   3.95   4.55   0.867754692       TR2   AF171055   1.60   1.59   1.007806633       TR2   AF171055   1.53   1.69   0.90288023       TRAF6   NM_004620   1.25   1.38   0.902520712       TRAF6   NM_004620   1.33   1.62   0.825230675       TTF-1   U43203   1.57   1.92   0.818730798       TTF-1   U43203   1.59   1.97   0.8042506       TTF-I interacting   AF000560   0.93   1.01   0.912809508       peptide       TTF-I interacting   AF000560   0.92   1.02   0.908180051       peptide       TTF1   NM_007344   1.36   1.32   1.03206288       TTF1   NM_007344   1.21   1.33   0.908191402       TTP   M63625   1.47   1.69   0.871059069       TTP   M63625   1.45   1.78   0.812551459       tumor suppressor   AJ224819   0.97   0.96   1.010680445       tumor suppressor   AJ224819   0.94   0.94   1.002997158       twist   X91662   1.15   1.30   0.889607419       twist   X91662   1.14   1.32   0.862171118       TZFP   NM_014383   1.61   1.57   1.026900096       TZFP   NM_014383   1.31   1.62   0.806125978       ubiquitin   M26880   1.25   1.29   0.968558812       ubiquitin   M26880   1.20   1.38   0.866123555       UBP1   NM_014517   1.16   1.39   0.837548498       UBP1   NM_014517   1.05   1.31   0.801834157       UKLF   AB015132   0.94   1.15   0.812199016       UKLF   AB015132   0.91   1.13   0.807110731       UsF1   X55666   0.92   0.77   1.202641159       UsF1   X55666   0.90   1.16   0.779296001       UsF2   X90824   1.70   1.51   1.12444728       UsF2   X90824   1.49   1.47   1.010033818       UTF1   NM_003577   0.78   0.92   0.852557876       UTF1   NM_003577   0.75   0.88   0.846901451       Vax-2   Y17791   1.95   1.73   1.125466134       Vax-2   Y17791   1.50   1.58   0.944890049       VDR   NM_000376   2.14   1.94   1.102535767       VDR   NM_000376   2.17   1.98   1.096166462       Vimentin   X56134   0.85   0.82   1.03779146       Vimentin   X56134   0.77   0.78   0.995470101       VSX1   NM_014588   1.19   1.38   0.862794625       VSX1   NM_014588   1.14   1.36   0.838036984       WAVE2   AB026542   1.37   1.57   0.873152446       WAVE2   AB026542   1.34   1.56   0.8602453       Whn   Y11746   0.95   1.05   0.89877812       Whn   Y11739   0.98   1.10   0.8889781       winged-helix   AF055080   1.80   1.62   1.112375194       TFforkhead 5       winged-helix   AF055080   1.64   1.65   0.995925632       TFforkhead 5       XB   U52701   0.93   1.00   0.931696975       XB   U52701   0.86   0.99   0.874287286       XBP1   NM_005080   1.32   1.48   0.894006132       XBP1   NM_005080   1.29   1.50   0.861985033       XG   Z48514   0.94   1.07   0.879021004       XG   Z48514   0.94   1.11   0.844934408       XPE-BF   U32986   1.23   1.06   1.157546744       XPE-BF   U32986   1.11   1.18   0.939655721       XPOT   NM_007235   0.93   1.04   0.888739099       XPOT   NM_007235   0.91   1.09   0.833312043       YAF2   U72209   1.78   1.60   1.115424048       YAF2   U72209   1.29   1.55   0.831250433       YPT3   X79780   1.04   1.04   0.999551657       YPT3   X79780   0.91   1.09   0.841560488       YWHAZ   NM_003406   1.42   1.48   0.955552146       YWHAZ   NM_003406   1.34   1.45   0.924713154       ZFD25   AB027251   1.38   1.47   0.935259419       ZFD25   AB027251   1.38   1.59   0.867549237       ZFM1   D26120   1.38   1.52   0.904756638       ZFM1   D26120   1.32   1.51   0.870056053       ZFN3   X60153   1.11   1.27   0.873020321       ZFN3   X60153   1.08   1.27   0.84639825       ZFN5128   NM_014347   1.68   1.48   1.132667677       ZFN5128   NM_014347   1.69   1.51   1.116327465       ZFP161   NM_003409   1.54   1.51   1.021814742       ZFP161   NM_003409   1.53   1.56   0.977142745       ZFP36   NM_003407   1.35   1.21   1.119420521       ZFP36   NM_003407   1.40   1.26   1.107958549       ZFP37   NM_003408   2.85   3.53   0.806477053       ZFP37   NM_003408   3.00   3.78   0.795656333       ZFS-2   D70832   1.25   1.31   0.960341853       ZFS-2   D70832   1.19   1.34   0.887098454       zinc finger factor GKLF   AF105036   2.60   2.44   1.066684361       zinc finger factor GKLF   AF105036   2.21   2.60   0.850960542       ZK1   NM_005815   1.09   1.29   0.849600519       ZK1   NM_005815   1.13   1.34   0.848599298       ZMPSTE24   NM_005857   1.59   1.96   0.807467602       ZMPSTE24   NM_005857   1.64   2.04   0.804181945       ZNF   AF024700   1.37   1.42   0.968200406       ZNF   AF024700   1.25   1.43   0.877660819       ZNF   AF024702   2.44   2.27   1.071242218       ZNF   AF024702   2.13   2.46   0.864203489       ZNF   AF024708   0.85   1.06   0.803894737       ZNF   AF024708   0.88   1.10   0.795504238       ZNF   AF244088   0.96   1.18   0.80824225       ZNF   AL359576   1.96   2.40   0.816139265       ZNF   AL359576   1.97   2.45   0.804419877       ZNF   L14787   0.81   0.94   0.858334842       ZNF   L14787   0.77   0.99   0.776247563       ZNF   L14843   1.04   1.21   0.859382421       ZNF   L14843   1.00   1.22   0.819499696       ZNF   M77171   0.87   1.07   0.819786317       ZNF   M77171   0.84   1.06   0.788842997       ZNF   M77172   1.11   1.29   0.86138076       ZNF   M77172   1.10   1.31   0.841409825       ZNF   U69645   1.02   1.11   0.923798753       ZNF   U69645   1.01   1.10   0.92309697       ZNF   U90919   1.91   2.41   0.791009945       ZNF   X16282   1.04   1.06   0.976817907       ZNF   X16282   0.97   1.08   0.896468376       ZNF H140   U80232   1.31   1.38   0.951857602       ZNF H140   U80232   1.25   1.46   0.852470368       ZNF RIZ   U17838   1.37   1.49   0.919856161       ZNF RIZ   U17838   1.33   1.52   0.878560838       ZNF10   NM_003419   1.14   1.24   0.918736842       ZNF10   NM_003419   1.06   1.25   0.852019812       ZNF124   NM_003431   1.66   1.70   0.976675202       ZNF124   NM_003431   1.69   1.79   0.942839506       ZNF131   U09410   4.06   3.16   1.287565844       ZNF131   U09410   3.52   3.10   1.135482919       ZNF132   NM_003433   1.58   1.92   0.819592954       ZNF132   NM_003433   1.39   1.80   0.770618048       ZNF133   NM_003434   1.00   1.08   0.92665805       ZNF133   NM_003434   0.98   1.07   0.917239309       ZNF133   U09366   1.59   1.48   1.074070972       ZNF133   U09366   1.44   1.60   0.901250209       ZNF134   NM_003435   0.87   1.03   0.842143011       ZNF134   NM_003435   0.89   1.11   0.803684073       ZNF135   NM_003436   1.21   1.31   0.927158596       ZNF136   NM_003437   1.76   1.84   0.953483104       ZNF136   NM_003437   1.71   1.96   0.871707485       ZNF139   U09848   1.82   2.14   0.854333258       ZNF139   U09848   1.88   2.25   0.83696718       ZNF140   NM_003440   1.18   1.31   0.902148538       ZNF140   NM_003440   1.10   1.38   0.795943758       ZNF141   NM_003441   0.94   1.10   0.852952765       ZNF141   NM_003441   0.97   1.14   0.851266923       ZNF143   NM_003442   1.23   1.38   0.888983121       ZNF143   NM_003442   1.25   1.41   0.88328255       ZNF144   NM_007144   1.39   1.50   0.928320948       ZNF144   NM_007144   1.37   1.47   0.926533504       ZNF146   NM_007145   2.27   2.48   0.916337136       ZNF146   NM_007145   2.13   2.64   0.805090416       ZNF154   U20648   1.01   1.10   0.91658232       ZNF154   U20648   0.98   1.10   0.890033893       ZNF157   NM_003446   3.06   3.63   0.842644802       ZNF157   NM_003446   3.32   4.07   0.815095843       ZNF169   U28251   1.07   1.06   1.007079353       ZNF169   U28251   0.99   1.12   0.884849008       ZNF173   NM_003449   1.76   1.84   0.954247529       ZNF173   NM_003449   1.69   1.91   0.885869838       ZNF174   U31248   1.05   1.11   0.946809357       ZNF174   U31248   0.98   1.07   0.916147357       ZNF175   NM_007147   1.42   1.58   0.896913462       ZNF175   NM_007147   1.37   1.66   0.824940576       ZNF177   NM_003451   1.35   1.31   1.030771696       ZNF177   NM_003451   1.16   1.36   0.850314531       ZNF180   NM_013256   0.97   1.13   0.856084978       ZNF180   NM_013256   0.97   1.18   0.824583936       ZNF186   NM_012480   1.05   1.14   0.913656108       ZNF186   NM_012480   0.99   1.11   0.892164294       ZNF191   AF016052   3.91   4.38   0.892949504       ZNF191   AF016052   4.30   5.22   0.823076704       ZNF200   NM_003454   1.53   1.36   1.124250225       ZNF200   NM_003454   1.47   1.43   1.02397083       ZNF211   NM_006385   2.54   2.24   1.133216101       ZNF211   NM_006385   2.36   2.13   1.105677798       ZNF214   NM_013249   1.12   1.35   0.833321399       ZNF214   NM_013249   1.15   1.43   0.806432749       ZNF215   NM_013250   1.09   1.24   0.879083204       ZNF215   NM_013250   1.13   1.35   0.837769383       ZNF216   AF062073   6.28   6.85   0.916789497       ZNF216   AF062073   6.12   6.94   0.882430365       ZNF22   NM_006963   1.06   1.27   0.835382221       ZNF22   NM_006963   1.05   1.29   0.80987367       ZNF220   NM_006766   1.16   1.31   0.88697634       ZNF220   NM_006766   1.15   1.35   0.848209348       ZNF223   NM_013361   1.29   1.44   0.90055118       ZNF223   NM_013361   1.25   1.45   0.865757643       ZNF228   NM_013380   1.13   1.10   1.028423144       ZNF228   NM_013380   0.84   1.00   0.838339028       ZNF229   AF192979   1.44   1.74   0.826578529       ZNF229   AF192979   1.41   1.76   0.802898585       ZNF231   NM_003458   1.29   1.38   0.933778707       ZNF231   NM_003458   1.24   1.42   0.875912367       ZNF232   NM_014519   3.91   3.54   1.103967871       ZNF232   NM_014519   3.65   3.40   1.074957509       ZNF232   AF080171   0.94   1.07   0.871430609       ZNF232   AF080171   0.92   1.08   0.856315576       ZNF258   NM_007167   3.65   2.56   1.429969861       ZNF258   NM_007167   2.86   2.23   1.280364117       ZNF261   NM_005096   2.03   2.19   0.929608653       ZNF261   NM_005096   1.79   2.05   0.873798627       ZNF297   NM_005453   1.40   1.66   0.844649054       ZNF297   NM_005453   1.39   1.65   0.841507575       ZNF31   U71600   0.91   1.13   0.804205241       ZNF31   U71600   0.89   1.16   0.770222697       ZNF35   NM_003420   1.53   1.57   0.977397734       ZNF35   NM_003420   1.52   1.62   0.938058006       ZNF37A   X69115   0.96   1.05   0.915518905       ZNF37A   X69115   0.94   1.13   0.835188396       ZNF41   M92443   1.52   1.91   0.798258529       ZNF41   M92443   1.53   1.99   0.771414141       ZNF41   X60155   0.99   1.06   0.934017616       ZNF41   X60155   1.01   1.10   0.917673489       ZNF47   U71601   1.03   1.18   0.872466879       ZNF47   U71601   0.96   1.14   0.8440485       ZNF7   NM_003416   1.04   1.17   0.895223602       ZNF7   NM_003416   1.07   1.23   0.869409968       ZNF8   M29581   0.94   1.00   0.940042921       ZNF8   M29581   0.84   0.94   0.89819251       ZNF80   NM_007136   2.05   1.92   1.064684732       ZNF80   NM_007136   1.98   1.93   1.024108326       ZNF85   NM_003429   1.27   1.39   0.915903902       ZNF85   NM_003429   1.14   1.42   0.797896136       ZNF91   NM_003430   1.09   1.09   1.002040082       ZNF91   NM_003430   1.04   1.07   0.975112741       ZNFB7   U34249   1.41   1.47   0.955940013       ZNFB7   U34249   1.34   1.50   0.893216374       ZNFN1A3   NM_012481   1.17   1.06   1.108208901       ZNFN1A3   NM_012481   1.17   1.06   1.100020165       ZNK75a   X91826   0.99   1.18   0.840732485       ZNK75a   X91826   0.98   1.24   0.792918773       ZRP-1   AF000974   4.16   4.74   0.87742034       ZRP-1   AF000974   4.06   4.99   0.813590373       ZYX   NM_003461   1.40   1.36   1.031031823       ZYX   NM_003461   1.31   1.36   0.963983275                  
 
         [0089]    List of References  
         [0090]    1. Chen, Y., Dougherty, E. R., Bittner, M. L. (1997) J. Biomed. Optics 24: 364-374.  
         [0091]    2. Hegde, P., Qi, R., Abernathy, K., Gay, C., Dharap, S., Gaspard, R., Earle-Hughes, J., Snesrud, E., Lee, N., Quackenbush, J. (2000) Biotechniques 29:548-562.  
         [0092]    [0092] 3 . Yang M C, Ruan Q G, Yang J J, Eckenrode S, Wu S, McIndoe R A, She J X. (2001) Physiol Genomics 7:45-53.  
         [0093]    [0093] 4 . Schena M, Shalon D, Davis R W, Brown P O. (1995). Science 270:467-70.  
         [0094]    5. Cho Y J, Meade J D, Walden J C, Chen X, Guo Z, Liang P. (2001) Biotechniques 30:562-8, 570, 572  
         [0095]    [0095] 6 . Brown A J, Planta R J, Restuhadi F, Bailey D A, Butler P R, Cadahia J L, Cerdan M E, De Jonge M, Gardner D C, Gent M E, Hayes A, Kolen C P, Lombardia L J, Murad A M, Oliver R A, Sefton M, Thevelein J M, Tournu H, van Delft Y J, Verbart D J, Winderickx J, Oliver S G. (2001). EMBO J 20:3177-86.  
         [0096]    [0096] 7 . Chaib H, Cockrell E K, Rubin M A, Macoska J A. (2001) Neoplasia:43-52.  
         [0097]    [0097] 8 . Barbu V, Dautry F. (1989) Nucleic Acids Res17:7115  
         [0098]    [0098] 9 . Gaudette M F, Crain W R. (1991). Nucleic Acids Res. 19:1879-84.  
         [0099]    [0099] 10 . Horikoshi S, Fukuda K, Ray P E, Sawada M, Bruggeman L A, Klotman P E. (1992). Kidney Int. 42:764-9.  
         [0100]    [0100] 11 . Kerr M K, Churchill G A. (2001). Proc Natl Acad Sci U S A 98:8961-5  
         [0101]    [0101] 
     
       
       
         1 
         
           
             3  
           
           
             1  
             21  
             DNA  
             Artificial Sequence  
             
               Description of Artificial Sequence 
      Oligonucleotide  
             
           
            1 

cttatgaccc gcacttactc g                                               21 

 
           
             2  
             40  
             DNA  
             Artificial Sequence  
             
               Description of Artificial Sequence 
      Oligonucleotide  
             
           
            2 

cccgagccgc ctggataccg cagctaggaa taatggaata                           40 

 
           
             3  
             40  
             DNA  
             Artificial Sequence  
             
               Description of Artificial Sequence 
      Oligonucleotide  
             
           
            3 

tctcgattcc gtgggtggtg gtgcatggcc gttcttagtt                           40