THE JOURNAL OF BIOLOGICAL CHEMISTRY© 2002 by The American Society for Biochemistry and Molecular Biology, Inc.

Vol. 277, No. 16, Issue of April 19, pp. 14048 –14052, 2002
Printed in U.S.A.

Genome-wide Transcriptional Orchestration of Circadian Rhythms
S
in Drosophila*□
Received for publication, December 27, 2001, and in revised form, February 15, 2002
Published, JBC Papers in Press, February 19, 2002, DOI 10.1074/jbc.C100765200

Hiroki R. Ueda‡§¶储, Akira Matsumoto¶**, Miho Kawamura§, Masamitsu Iino‡,
Teiichi Tanimura**‡‡, and Seiichi Hashimoto§
From the ‡Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo
113-0033, §Molecular Medicine Research Laboratories, Institute for Drug Discovery Research, Yamanouchi
Pharmaceutical Co., Ltd., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, and the **Department of Biology, Faculty of
Science, Kyushu University, Ropponmatsu, Fukuoka 810-8560, JapanThe use of Drosophila has been at the forefront of studies ofthe molecular and genetic basis of circadian rhythms (1). A
number of clock genes have been identified in Drosophila, andinterlocked per-tim and Clk feedback loops are now thought tounderlie the central molecular machinery of circadian rhythms(2, 3). However, we still do not know how expression of thewhole genome is orchestrated by the circadian mechanism nor
have we identified all the genes involved. One comprehensive
way to find out all the rhythmically expressed genes is to utilize
microarray. A number of genes regulated in a circadian manner
have been identified in Arabidopsis and mammalian cultured* This work was performed as a part of a research and development
project of the Industrial Science and Technology Program supported by
NEDO (New Energy and Industrial Technology Development Organization) and was also supported by grants from the Ministry of Education, Science, Sports and Culture of Japan (to T. T. and A. M.). The costsof publication of this article were defrayed in part by the payment ofpage charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate thisfact.
□
S The on-line version of this article (available at http://www.jbc.org)
contains Tables I–VIII.
¶ Both authors contributed equally to this work.
储 To whom correspondence may be addressed. Tel.: 81-298-54-1524;
Fax: 81-298-54-1669; E-mail: hiro@m.u- tokyo.ac.jp.
‡‡ To whom correspondence may be addressed. Tel.: 81-92-726-4759;
Fax: 81-92-726-4625; E-mail: tanimura@rc.kyushu-u.ac.jp.

cells (4, 5). Since information about all the possible transcription units is available in Drosophila (6, 7), we can extensively
analyze the data for all the genes relating to their function.
Functions of identified genes can be analyzed using various
genetic tool and databases (9 –11) available in Drosophila.
EXPERIMENTAL PROCEDURES

Strain and Sample Preparations—white1118 was used as a wild-typestrain, and ClkJrk was also used (11). Flies were reared in a regime of
12 h of light followed by 12 h of darkness (LD),1 and collected every 4 hover 2 days. Total RNA was prepared from 100 heads of 1-week-old
adult males and females using the Fast RNA kit (BIO 101, Inc.) followed by DNase treatment. Double-stranded cDNA was synthesizedfrom 10 ␮g of total RNA using Superscript II reverse transcriptase(Invitrogen) and was used as a template to synthesize biotin-labeledcRNA by in vitro transcription using an ENZO BioArray High Yield
RNA transcript labeling kit. Amplified cRNA was fragmented and hybridized to GeneChip Drosophila arrays (Affymetrix, Santa Clara, CA)
for 16 h at 45 °C. Hybridized arrays were washed, stained, and scanned
using a Hewlett-Packard GeneArray Scanner. Affymetrix GeneChip
software was used to determine the average difference between perfectly matched oligonucleotide probes and single base pair mismatches
for each probe set. Data were then scaled globally such that the total
intensity of each microarray is equal. The resulting hybridization intensity values reflect the abundance of a given mRNA relative to thetotal RNA population and were used in all subsequent analyses. Quantitative PCR was performed using the ABI Prism 7700 and SYBR Green
reagents (Applied Biosystems).
Analysis of Cycling Genes—We examined gene expression profiles
under LD using two successive filters: a periodic filter to extract genes
with periodic expression patterns and a deviation filter to identify genes
where the changes were above background level.
First, to extract genes with periodic expression pattern, we empirically tested for statistically significant cross-correlation between thetemporal expression profiles of each probe set and cosine waves ofdefined period and phases. We prepared cosine waves of nine test
periodicities (␶) from 20 to 28 h in increments of 1 h. Cosine waves ofeach test period were considered over 60 phases (i.e. peaks at 60 equally
spaced times in the defined period), yielding a total of 540 test cosine
waves. Statistical significance was assessed by an empirical procedure.
We generated ⬃14,000 (the same number of probe sets) normally distributed random expression profiles. Then we calculated correlation
between the random profiles and each of the 540 test cosine waves.
Standard deviations and averages of cross-correlation were virtuallyequal for 540 cosine filters despite their different periods and phases.
Thus, we searched for the common cut-off correlation of these cosine
filters so that 95% of random expression profiles were filtered out after
passing 540 parallel cosine filters. We determined this value as 99.8%
probable correlation. This analysis is independent of signal strengthand imposes no minimal change in amplitude.
Next, to further extract genes whose variation was above background, we determined the noise level associated with a series of ex1
The abbreviations used are: LD, 12 h of light followed by 12 h ofdarkness; DD, constant dark; RT, reverse transcription; GABA, ␥-aminobutyric acid.

14048

This paper is available on line at http://www.jbc.org

Downloaded from http://www.jbc.org/ at University of Tokyo Library on May 29, 2017

Circadian rhythms govern the behavior, physiology,
and metabolism of living organisms. Recent studies
have revealed the role of several genes in the clock
mechanism both in Drosophila and in mammals. To
study how gene expression is globally regulated by theclock mechanism, we used a high density oligonucleotide probe array (GeneChip) to profile gene expression
patterns in Drosophila under light-dark and constantdark conditions. We found 712 genes showing a daily
fluctuation in mRNA levels under light-dark conditions,and among these the expression of 115 genes was still
cycling in constant darkness, i.e. under free-running
conditions. Unexpectedly the expression of a large number of genes cycled exclusively under constant darkness. We found that cycling in most of these genes waslost in the arrhythmic Clock (Clk) mutant under lightdark conditions. Expression of periodically regulated
genes is coordinated locally on chromosomes where
small clusters of genes are regulated jointly. Our findings reveal that many genes involved in diverse functions are under circadian control and reveal the complexity of circadian gene expression in Drosophila.

Genome-wide Orchestration of Circadian Rhythms

14049

perimental procedures for each probe set. Two replicate samples (i.e.
two sets of 100 fly heads collected independently at the same time of theday) were hybridized to two GeneChips. The standard deviation of thetwo signal intensities for each probe set was calculated and used asnoise deviation (␴) in subsequent analysis. Expression profiles which,over the 12 time points, show a standard deviation (s) greater thannoise deviation (␴) with 95% significance are classified as “changing.”
95% probability cut-off values are determined from ␹2 (chi-square)
distribution with 11 degrees of freedom ((12 ⫺ 1) s2/␴2 ⬎ 19.6751).
To estimate the false positive rate, we generated ⬃14,000 (the same
number of probe sets) random expression profiles that were normally
distributed using the noise deviations as determined above. Then we
filtered these random expression profiles using two successive filters.
Random profiles produced 27 genes classified as “periodically changing.” We assume that this estimates the false positive rate (i.e. 3.8% of
all genes identified would be false positives).
To analyze periodicity of gene expression profiles under constantdark (DD), we used damping cosine curves as test waves. We prepareddamping cosine waves of four decay rates (k) from 0.0/h (no damping) to
0.03/h (half-life is 23.0 h) in increments of 0.01/h. Each was consideredat nine test periodicities and over 60 phases as described above. We
used the same cut-off cross-correlation values and the same deviation
filters as in LD analysis.
Phase Analysis—To determine the phase of cycling genes, we tested
for correlation between the temporal expression profiles of each geneand 24-h period cosine waves at 60 different phases. We estimated thephase of each cycling gene from the phase of the cosine wave with which
it was correlated most closely.
Determination of Statistical Significance for Rhythmic Biological
Processes and Periodically Regulated Molecules—We classified the cycling genes by biological process category in the Gene Ontology database (9). For each category, we calculated the probability of finding atleast r periodically regulated genes from the category size (n) using the
cumulative hypergeometric probability distribution. Probability isgiven by:

冘 共 兲共共 兲 兲r⫺1

Probability ⫽ 1 ⫺

l⫽1

n
l

N⫺n
R⫺l

N
n

We also performed similar analyses using the LIGAND metabolic
database (9). We mapped cycling genes into the metabolic network in
Drosophila and calculated the probability for observing at least r cycling genes within n enzymes metabolizing the same molecule using the
cumulative hypergeometric probability distribution as above.
Analysis of ClkJrk—For each gene, expression levels in ClkJrk mutants were averaged with those in wild-type flies. Both were kept in LD
conditions, and equivalent points in the light-dark cycle were compared.
Genes were classified as “up-regulated” if expression was at least 2
times higher in the mutant and “down-regulated” if expression was
least 2 times lower in the mutant. Otherwise genes were classified as“unchanged.”
Mapping of Periodically Regulated Genes and Calculation of Chromosome Correlation Maps—Among 14,010 probes on the GeneChip, 44
probes are for control, and 299 probes map to multiple genes. The other
13,667 probes map to single genes. Among these, there are several
redundant probe sets that map to the same gene, leaving 13,282 nonredundant probes. 12,795 of these match in FlyBase ID (10) to identified
genes from Release 2 Drosophila genomic sequences (6, 7). We identified the chromosomal positions of all 12,795 genes using the BLASTN
algorithm. Using the chromosomal positions obtained above, we
mapped the genes belonging to each Class I, II, and III on chromosomes.
To detect co-regulated regions, we calculated the correlation between
expression patterns under LD conditions of genes on the same chromosome as described elsewhere (12). To identify significantly co-regulated
regions, we calculated the average correlation of six adjacent genes andcompared it with the average correlation of six nonadjacent genes asbackground. There were 140 chromosomal regions where the averagecorrelation of the six adjacent genes was more than 3.5 standard deviations from background, i.e. the mean average correlation of six nonadjacent genes. This analysis showed that a substantial number ofadjacent sets have correlated expression patterns in comparison with
25 expected co-regulated regions derived from a control set of nonadjacent genes. Similar results were obtained from analysis of 2–10 adjacent genes. Among 140 chromosomal regions, 38 clusters of genes included periodically regulated genes. We also analyzed co-expressedregion under the DD condition and obtained similar results to the LD
condition.
RESULTS AND DISCUSSION

where N is the total number of genes within the genome, and R is thetotal number of periodically regulated genes. p values (⫺log10 (probability)) where the sum of probabilities is below 0.05 were consideredsignificant.

We have examined temporal patterns of gene expression
under LD and under DD using a GeneChip (Affymetrix) representing the entire genome (more than 13,500 genes) of Dro-

Downloaded from http://www.jbc.org/ at University of Tokyo Library on May 29, 2017

FIG. 1. Cycling of gene expression inwild-type flies kept under LD and DD
and in ClkJrk mutant flies under LD. a,a cluster image of 712 cycling genes under
LD. Data were normalized so that the average and the standard deviation of signal
intensities of 12 time points are 0.0 and 1.0,
respectively. For each gene, the 12 horizontal bars along the time axis represent a
48-h series of data. The genes were orderedby their peak time to help to visualize theextensive pattern of cycling. Bars are colored red for positive values and green for
negative values as shown in the upper color
code. b, a cluster image of 456 genes whose
expression is free-running under DD. The
details of representation are similar to a. cand d, phase distributions of the peak expression times of periodically regulated
genes under LD (c) and DD (d) derived
from data on 712 and 456 periodically regulated genes under LD and DD, respectively. Two major populations have peaks
at around ZT10 and ZT20 under LD. Thesepeaks are not found in DD. e, periodic expression of per, tim, vri, Clk, cry, and tounder LD and DD in wild-type and in
ClkJrk mutant background flies under LD.
Data of LD and DD were normalized sothat the average signal intensity of 12 time
points was 1.0. For data in ClkJrk background, signal intensities of these genes
were divided by the average signal intensities under LD conditions. WT, wild type.

14050

Genome-wide Orchestration of Circadian Rhythms

sophila melanogaster. Flies were collected every 4 h over 2 days
both in LD and DD, and biotin-labeled probes made from cDNAfrom 100 heads were used for hybridization. We estimate thatthe expression of 6,061 genes (43.4% of all genes) was detectedon GeneChip. The number of genes detected here is thought tobe delimited by the detection method using GeneChip, andthere should be additional cycling genes expressed at a lower
level or in a small number of cells. Data were analyzed throughtwo sequential statistical filters, and 712 genes (5.3% of thewhole genome) were classified as periodically regulated genes
in LD (Fig. 1a). This is likely to be a minimum number for thegenes that are periodically regulated; the number may increase
if a different filtration analysis was applied. Our analyses
might not detect genes that cycle in some cells but not inothers, and moreover, it is technically difficult to monitor genes
with very low levels of transcription. The number of periodically regulated genes in Drosophila is similar to that reported
from Arabidopsis under constant light (4), in which 6% of genes
investigated are rhythmic, but is in contrast to cyanobacteria,
in which nearly all genes are expressed periodically (13). We
found that genes implicated in circadian rhythms, including
period (per) (14), timeless (tim) (15), Clock (Clk) (11), vrille (vri)(16), cryptochrome (cry) (17), and takeout (to) (18), cycled withhigh amplitude and in similar phase, as previously reported,
validating our experimental and statistic procedures (Fig. 1e).
We analyzed the phase of periodically regulated genes at aresolution of 0.4 h and found two peaks around ZT10 and ZT20
(Fig. 1c). The peaks may reflect the after-effect of the change
from dark to light and light to dark since significant peaks wereabsent under the constant dark condition (Fig. 1d). The peakphases of the clock genes, Clk, cry, per, vri, tim, and to, were notat these times. We then analyzed the gene expression underDD (Fig. 1b) and found that 115 genes of 712 were still periodically regulated in the free-running condition (Class I, periodically regulated both in LD and DD). The remaining 597
genes were judged to be periodically regulated only in LD(Class II). Surprisingly 341 genes that were not judged asperiodically regulated under LD were, however, periodicallyregulated under DD (Class III). Their cyclings might have been
suppressed or masked under LD as suggested from behavioral
experiments (19). In our classification of genes we should notethat because we used a strict filter to identify periodicallyregulated genes, genes judged to be not cycling might in fact
cycle with low amplitude. Lists of all genes in each class may befound in Supplemental Tables I–III. After completion of ourwork two similar works using GeneChip were published (20,21). Their findings are similar to ours, but there are several
differences, specifically the Class II and III genes were notmentioned in other studies. We think that the major differences are the numbers of sampling and statistical analyses. We
analyzed data for 2 days both under LD and DD, while theprevious studies analyzed data only for 1 day in each light
condition. Several interesting periodically regulated genes
were identified from the three classes, I, II, and III (Fig. 2). The
reliability of GeneChip data was assessed by quantitative RTPCR analyses, which confirmed that both methods yielded
similar data. A novel candidate of clock genes, Pdp1, showing arobust cycling (Fig. 2a), encodes a transcription factor with

Downloaded from http://www.jbc.org/ at University of Tokyo Library on May 29, 2017

FIG. 2. Three classes of periodicallyregulated genes and validation of GeneChip data by quantitative RT-PCR
using wild-type flies (WT) under LD
and DD and ClkJrk (Clk) mutant flies
under LD. a, Class I genes cycling bothin LD and DD; b, Class II genes cycling
only in LD; c, genes cycling in DD but notin LD. In each class, data are shown for
two to three genes, the rhythmic expression of which was found in this study.
Upper curves in a, b, and c are based on
the GeneChip analyses; lower curves are
based on the quantitative PCR analyses.
Pdp1, PAR domain protein encoding atranscription factor; Pdh, photoreceptor
dehydrogenase; trpl, transient receptor
potential-like encoding a Ca2⫹ channel;
inaC, inactivation no after-potential C encoding a protein kinase C; inaD, inactivation no after-potential D encoding a structural protein containing a PDZ domain;
Cyp4e2, cytochrome P450-4e2.

Genome-wide Orchestration of Circadian Rhythms

14051

homology to vri (16). Most of the genes we found to cycle could
be classified according to the category of their “biological process” as defined in the Gene Ontology database (8) (Supplemental Tables IV and V). Phototransduction is one such category,
which includes a significant number of periodically regulated
genes. Two of these were Class I genes. Photoreceptor dehydrogenase, Pdh, also showed a clear cyclical expression (Fig. 2).
One retinoid-binding protein (CG5958) was periodically expressed with peak at dusk, while the other retinoid-binding
protein (CG10657) belonging to Class II was cycling with almost opposite phases. A number of genes belonged to Class II.
Three opsins, Rh3, Rh4, and Rh6, which express in the central
rhabdomeres of the compound eye’s ommatidia, showed rhythmic expression. Another opsin, Rh5, belonged to Class III. The
ninaA gene encoding cyclophilin, which transports opsins fromendoplasmic reticulum to microvilli membrane, also showedrhythmic expression. Molecules associating with Ca2⫹ signaltransduction in the photoreceptors, inaC, inaD, and trpl, also
cycled (Fig. 2b). The expression of most genes listed above
peaked in the morning, whereas Rh6 and trpl peaked in theevening. Visual sensitivity is controlled by a circadian rhythm
in insects (22), and it would therefore be interesting to know
how cyclical changes in these genes influence photoreceptor
structure and function.
We also used the LIGAND metabolic database (9) to examine
the functional significance of periodically regulated genes (Supplemental Tables VI and VII). Enzymes and transporters involved in metabolism or function of glutamate and GABA wereperiodically regulated. Eaat1, CG5618, and CG7470 are ClassI genes, and Gdh, black, CG4233, and CG7433 are Class II
genes. Gs1 belongs to Class III. All genes except CG4233
showed robust rhythmicity with peaks in the dark phase. In
mammals, glutamate (23) and GABA (24) are neurotransmitters associated with clock function. These molecules mimic

the dark pulse to a circadian rhythm in the optic lobe ofMusca (25). In Drosophila, one type of glutamate receptor ishighly enriched in pacemaker neurons (26), and our datasuggest glutamate and GABA might have a role in the circadian mechanism. In the light of a recent finding that theredox state of NAD cofactors is involved in circadian rhythms(27), it is interesting that many enzymes related to NAD⫹,
NADH, NADP⫹, and NADPH metabolism were periodicallyregulated. There are 16 periodically regulated genes directly
associated to the synthesis of these nicotinamide nucleotides.
Three are in Class I, and the remaining 13 are in Class II.
Their peaks expression occurred in three phases under LD:
noon, dusk, and night.
We next examined the cycling of gene expression in thearrhythmic mutant of the Clock (Clk) gene (11) under LD. Our
study showed that many genes are cycling only in LD, and wethen asked whether the cyclings of the Class II genes are
merely a reflection of light responses. Homozygous ClkJrk mutants show completely arrhythmic locomotor behavior underDD (11). CLK is a transcription factor and activates clockregulated genes (1, 2, 11). In the Clk mutant, periodically
expression of all the clock genes disappeared (Fig. 1e), and only
a few genes were judged to cycle under LD (7, 16, and 23 genes
in Class I, II, and III, respectively; Supplemental Table VIII). It
is possible that the cycling genes in the ClkJrk mutant may
represent genes controlled by a possible CLK-independent
mechanism. We did not analyze the cycling pattern with two
peaks in a day. If cycling is simply controlled by light-on and-off, it shows a pattern with dual peaks in a day. We did notinvestigate this possibility, but genes belonging to the Class III
may have such a property. Further studies are necessary toinvestigate this possibility.
Our results suggest that the cycling of the Class II genes is
not merely a result of light exposure during LD but is underDownloaded from http://www.jbc.org/ at University of Tokyo Library on May 29, 2017

FIG. 3. Global chromosomal profiles of periodic gene expression. a, correlation map for gene clusters that included the Class I genes on
the right arm of the second chromosome. The green block at the center indicates the group of six adjacent co-expressing genes, including cytochrome
P450, Cyp6a17 (Class I), Cyp6a23, Cyp6a19, Cyp6a9, Cyp6a20, and Cyp6a21. The numbers along the matrix represent the gene number along thechromosome. Green squares indicates a positive correlation; red squares indicate a negative correlation. b, the six cytochrome P450 genes that areperiodically co-regulated under LD and DD. Cyp6a17 is represented by the green line with the highest peak at a time point of 25 h. c, correlation
map for gene clusters that included the Class I genes but that have no functional relatedness to each other. d, three genes on the third chromosome(CG11891, which belongs to Class I, CG11889, and CG10513) showed similar rhythmic expressions in LD, and periodic expression of these genes
also persists under DD. Data for CG11889 under DD is not shown here as they included a few negative values. e, correlation map for gene clusters
that included the three Class II genes on the left arm of the third chromosome. f, CG7646, CG7654, and CG7433 are Class II genes, and theirneighboring gene, neurocalcin, showed a similar expression pattern in LD. WT, wild type.

14052

Genome-wide Orchestration of Circadian Rhythms
Although cycling gene expression is not always essential for
circadian function, in clock genes such as cyc (29) and doubletime (30) our study has established the candidacy of many
candidate genes that might be implicated in circadian mechanisms. Further work using genetic tools available in Drosophila should help to explore the function of these genes with theprospect of leading to a greater understanding of the molecularbasis of circadian rhythms in all organisms.
Acknowledgments—We are grateful to Michael Rosbash and Jeffrey
C. Hall for the ClkJrk strain. We thank Shigeru Iwase for computational
analysis; Satoko Hayashi, Tomoko Kojima, Toshie Katakura, Yuko
Mitsuiki, and Makiko Haruta for technical assistance; and MasamiHorikoshi and Takashi Umehara for hospitality in the use of theirlaboratory. We also thank Hideo Iwasaki and Kenji Tomioka for discussion and Jennifer Hallinan and Ian Meinerzhagen for comments on
the manuscript.
REFERENCES
1. Dunlap, J. C. (1999) Cell 96, 271–290
2. Glossop, N. R., Lyons, L. C., and Hardin, P. E. (1999) Science 286, 766 –768
3. Ueda, H. R., Hagiwara, M., and Kitano, H.(2001) J. Theor. Biol. 210, 401– 406
4. Harmer, S. L., Hogenesch, J. B., Staume, M., Chang, H. S., Han, B., Zhu, T.,
Wang, X., Kreps, J. A., and Kay, S. A. (2000) Science 290, 2110 –2113
5. Grundschober, C., Delaunay, F., Puhlhofer, A. Triqueneaux, G., Laudet, V.,
Bartfai, T., and Nef, P. (2001) J. Biol. Chem. 276, 46751– 46758
6. Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D.,
Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., etal. (2000) Science 287, 2185–2195
7. Myers, E. W., Sutton, G. G., Delcher, A. L., Dew, I. M., Fasulo, D. P., Flanigan,
M. J., Kravitz, S. A., Mobarry, C. M., Reinert, K. H., Remington, K. A., et al.
(2000) Science 287, 2196 –2204
8. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M.,
Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) Nat. Genet.
25, 25–29
9. Goto, S., Nishioka, T., and Kanehisa, M. (2000) Nucleic Acids Res. 28, 380 –382
10. FlyBase (1999) Nucleic Acids Res. 27, 85– 88
11. Allada, R., White, N. E., So, W. V., Hall, J. C., and Rosbash, M. (1998) Cell 93,
791– 804
12. Cohen, B. A., Mitra, R. D., Hughes, J. D., and Church, G. M. (2000) Nat. Genet.
26, 183–186
13. Liu, Y., Tsinoremas, N. F., Johonson, C. H., Lebedeva, N. V., Golden, S. S.,
Ishiura, M., and Kondo, T. (1995) Genes Dev. 9, 1469 –1478
14. Hardin, P. E., Hall, J. C., and Rosbash, M. (1990) Nature 343, 536 –540
15. Sehgal, A., Price, J. L., Man, B., and Young, M. W. (1994) Science 263,
1603–1606
16. Blau, J., and Young, M. W. (1999) Cell 99, 661– 671
17. Emery, P., So, W. V., Kaneko, M., Hall, J. C., and Rosbash, M. (1998) Cell 95,
669 – 679
18. So, W. V., Sarov-Blat, L., Kotarski, C. K., McDonald, M. J., Allada, R., andRosbash, M. (2000) Mol. Cell. Biol. 20, 6935– 6944
19. Mrosovsky, N. (1999) Chronobiol. Int. 16, 415– 429
20. Claridge-Chang, A., Wijnen, H., Naef, F., Boothroyd, C., Rajewsky, N., andYoung, M. W. (2001) Neuron 32, 657– 671
21. McDonald, M. J., and Rosbach, M. (2001) Cell 107, 567–578
22. Chen, B., Meinertzhagen, I. A., and Shaw, S. R. (1999) J. Comp. Physiol. 185,
393– 404
23. Ding, J. M., Chen, D., Weber, E. T., Faiman, L. E., Rea, M. A., and Gillette,
M. U. (1994) Science 266, 1713–1717
24. Moore, R. Y., and Speh, J. C. (1993) Neurosci. Lett. 150, 112–116
25. Pyza, E., and Meinertzhagen, I. A. (1996) J. Comp. Physiol. 178, 33– 45
26. Volkner, M., Lenz-Bohme, B., Betz, H., and Schmitt, B. (2000) J. Neurochem.
75, 1791–1799
27. Rutter, J., Reick, M., Wu, L. C., and McKnight, S. L. (2001) Science 293,
510 –514
28. Crosio, C., Cermakian, N., Allis, C. D., and Sassone-Corsi, P. (2000) Nat.
Neurosci. 3, 1241–1247
29. Rutila, J. E., Suri, V., Le, M., So, W. V., Rosbash, M., and Hall, J. C. (1998) Cell
93, 805– 814
30. Price, J. L., Blau, J., Rothenfluh, A., Abodeely, M., Kloss, B., and Young, M. W.
(1998) Cell 94, 97–107

Downloaded from http://www.jbc.org/ at University of Tokyo Library on May 29, 2017

circadian control. Under LD, the expression levels of per, tim,
vri, and to were decreased relative to Clk (Fig. 1e), whereas Clk
and cry continue to express at a high level as previously shown(11, 17). Fig. 2 shows the expression patterns of seven genes in
ClkJrk. If the transcription level of a gene is lowered in ClkJrk,
the gene might be up-regulated by Clk, whereas if the level is
not affected, the gene might be regulated by a CLK-independent mechanism. The expression of about 6% of genes was decreased, while in about 3% of genes it was increased. In thelatter case, their transcription might normally be down-regulated by genes controlled by CLK. These results indicate that
CLK regulates transcription in many genes, but there are othergenes in which transcription is not directly controlled by CLK.
In addition some genes might be negatively regulated by CLK.
We do not think that these changes are caused by the genetic
background differences as we dealt with genes whose expression level changed over 2-fold or one-half. Our study thus
shows that a single mutation in such a central gene regulator
results in global but differential changes of gene expression.
We mapped the chromosomal locations of genes belonging toeach class (I, II, and III) and found that they were not randomly
distributed but clustered on chromosomes. There were 15 clusters where periodically regulated genes occupied a highly condensed chromosome interval. This suggests that temporal gene
expression might be locally regulated on chromosomes. To confirm this possibility, we calculated the correlation of temporal
expression pattern along the neighboring genes on all chromosomes and found 140 chromosomal regions where neighboring
genes are expressed with a similar pattern to each other.
Among them, 38 regions contained at least one periodicallyregulated gene. There were six genes in Class I, 24 in Class II,
and eight in Class III. For example, the expression patterns of
six neighboring genes belonging to the cytochrome P450 family,
located on the right arm of the second chromosome, are similar(Fig. 3, a and b). There is a region where genes are co-regulated, but their functions are unknown (Fig. 3, c and d). Moreover, we found that functionally unrelated genes are co-regulated (Fig. 3, e and f). These results suggest that the temporal
expression of neighboring genes is influenced by a periodicallyregulated gene. Searches of each class of periodically regulated
genes so far failed to reveal any common motifs in the nucleic
acid sequence along the putative regulatory region of each classof cycling genes. We found that the co-regulation of temporal
expression occurs even more globally. The co-regulated regions
were observed along the fourth chromosome at intervals of
about 5–10 genes (data not shown). The regular spacing suggests control at the level of higher order chromatin structure aspreviously reported in suprachiasmatic nuclei neurons (28).
These results suggest that gene expression on chromosomes is
globally regulated by circadian mechanisms, although we still
do not know their molecular bases. Coordinated gene regulation at the chromatin level might be an economical way inremodeling chromosome structures.
Our study thus reveals the complex transcriptional orchestration of genes under LD and DD conditions in Drosophila.

Supplemental Information for Ueda et al.

Table 1: Drosophila Genes Rhythmically Expressed Both in Light-Dark and Constant Dark Conditions.
Accession #Gene Name

Correlation(LD+DD)

Phase(LD)

Phase(DD)mRNA Levels in Clk(Clk/wt)

FBgn0014396

timeless

1.968914.8

15.2

Down (0.19061)

FBgn0040900

CG17777

1.94301

21.2

21.6

Down (0.133756)

FBgn0016076

vrille1.90589

13.6

12.4

Down (0.1759)

FBgn0024290

Slowpoke binding protein

1.90238

14.4

12.4

Not Changed (1.17702)

FBgn0023076

Clock

1.89791

2.

2.

Not Changed (1.61517)

FBgn0026314

UDP-glycosyltransferase
35b1.882432.

0.8

Not Changed (0.937727)

FBgn0025680

cryptochrome

1.87782

5.2

5.2

Not Changed (1.6446)

FBgn0039324

CG10553

1.87508

19.6

19.6

Not Changed (0.918862)

FBgn0032167

CG58531.8721516.

18.8

Not Changed (0.510791)

FBgn0031326

CG51561.85227

2.8

2.4

Down (0.403719)

FBgn0038184

CG92851.84608

1.6

0.4

Not Changed (1.01046)

FBgn0032022

CG14275

1.84465

14.

13.2

Not Changed (1.06334)

FBgn0036992

CG11796

1.82834

4.

1.2

Not Changed (1.20056)

FBgn0030422

CG15723

1.822321.6

20.8

Not Changed (0.668471)

FBgn0034115

CG16796

1.80734

20.8

0.4

Not Changed (0.548936)

FBgn0038862

CG57981.80607

12.4

12.

Down (0.429404)

FBgn0032886

CG93281.79906

22.

20.8

Not Changed (1.57588)

FBgn0038966

CG13848

1.79740.4

24.

Not Changed (0.585615)

FBgn0031913

CG59581.79351

10.4

11.2

Not Changed (1.28367)

FBgn0003068

period

1.792813.6

13.6

Not Changed (0.823371)

FBgn0039298

takeout

1.78783

23.6

23.2

Down (0.00711846)

FBgn0011693

Photoreceptor
dehydrogenase

1.78632.8

1.6

Not Changed (1.09725)

FBgn0034390

CG15093

1.78341

3.2

5.6

Not Changed (0.75899)

FBgn0033289

CG21211.77377

12.

12.

Not Changed (1.33584)

FBgn0031428

CG9886

1.7695

19.6

20.

Not Changed (0.948965)

FBgn0034108

CG37671.7611223.2

1.6

Not Changed (1.18085)

FBgn0023548

msta

1.76079

22.4

20.8

Not Changed (1.21929)

FBgn0016694

PAR-domain protein 1

1.7603114.

14.

Not Changed (0.578511)

FBgn0033464

CG14411.75884

22.4

21.6

Not Changed (0.724898)

FBgn0024289

Sorbitol dehydrogenase 1

1.75587

10.4

13.2

Not Changed (1.43016)

FBgn0010383

Cytochrome P45-18a1

1.75318

17.6

15.6

Down (0.4171)

FBgn0036975

CG56181.74869

22.

24.

Down (0.465337)

LD15411.3prime-hit

CG17100

1.74559

13.2

13.6

Not Changed (0.839869)

Supplemental Information for Ueda et al.
LD29569.3prime-hit

CG12790

1.74397

21.6

22.

Not Changed (1.15495)

FBgn0000723

Fps oncogene analog

1.74169

17.2

1.2

Not Changed (1.28634)

FBgn0034229

CG48471.74157

6.

5.2

Not Changed (1.1628)

FBgn0032739

CG15171

1.73872

14.4

12.

Not Changed (0.904992)

FBgn0040491

Buffy

1.73788

9.6

23.6

Not Changed (1.58313)

FBgn0038211

CG96491.73656

2.4

1.6

Not Changed (1.83911)

FBgn0039309

CG118911.73006

22.

21.2

Not Changed (0.801263)

FBgn0011768

Formaldehyde
dehydrogenase

1.72598

9.6

11.6

Not Changed (0.832379)

FBgn0035282

CG13936

1.72321

9.6

12.4

Down (0.244055)

FBgn0037290

CG11241.72075

7.6

7.6

Not Changed (0.790751)

FBgn0015872

Drip

1.71802

9.2

4.4

Not Changed (1.46769)

FBgn0015714

Cyp6a171.71544

23.6

0.8

Not Changed (1.01577)

FBgn0033821

CG10799

1.71527

19.6

22.

Not Changed (0.857952)

FBgn0034934

CG28271.71292

9.6

10.8

Down (0.467347)

GH1265.3prime-hit

CG12397

1.71054

18.8

21.2

Not Changed (0.894984)

FBgn0039084

CG10175

1.70787

17.6

19.2

Not Changed (0.866168)

FBgn0037865

CG18578

1.70703

4.4

2.4

Not Changed (1.20009)

FBgn0033675

CG88891.70439

2.8

23.6

Not Changed (1.2497)

FBgn0027593

BcDNA:GH03693

1.70365

17.6

10.

Up (2.52465)

FBgn0031971

CG72241.70198

18.8

17.2

Not Changed (1.1274)

FBgn0031808

CG95071.70127

18.4

17.2

Not Changed (1.659)

FBgn0036673

CG11915

1.69733

1.2

24.

Not Changed (1.26821)

FBgn0027055

COP9 complex homolog
subunit 3

1.69635

18.

3.6

Not Changed (0.828713)

FBgn0038212

CG9645

1.69464.4

2.8

Not Changed (1.14215)

FBgn0035985

CG3672

1.68791

23.6

0.4

Not Changed (0.750775)

FBgn0034706

CG11275

1.68698

21.6

23.2

Not Changed (0.578001)

FBgn0041001

CG144031.684222.8

22.4

Not Changed (1.03193)

LP11629.3prime-hit

CG34511.68388

18.

19.2

Not Changed (1.22562)

FBgn0038972

CG7054

1.68145

11.2

10.8

Not Changed (1.81932)

SD1469.3prime-hit

CG84681.68036

13.2

10.4

Not Changed (1.18721)

FBgn0037607

CG8036

1.67872

8.8

12.

Not Changed (0.983286)

FBgn0037515

CG3066

1.67825

0.4

24.

Not Changed (0.81568)

FBgn0036659

CG97011.67813

21.6

16.8

Not Changed (1.29681)

FBgn0039001

CG49191.67624

11.2

12.8

Not Changed (0.719025)

FBgn0036698

CG7724

1.67282

1.6

23.6

Not Changed (1.09218)

Supplemental Information for Ueda et al.
FBgn0034431

CG74171.67144

8.4

5.2

Not Changed (1.36717)

FBgn0038987

CG6926

1.67138.8

24.

Not Changed (0.910419)

FBgn0026439

Excitatory amino acidtransporter 1

1.66755

18.8

6.

Not Changed (0.998365)

FBgn0000711

flap wing

1.66573

0.8

23.6

Not Changed (1.06101)

FBgn0030258

CG1552

1.66379

23.2

0.8

Not Changed (0.870164)

FBgn0029534

CG5273

1.66197

0.8

23.2

Not Changed (0.701181)

FBgn0004210

puckered

1.65739

12.4

10.4

Not Changed (0.923931)

FBgn0033853

CG61451.65468

16.8

18.8

Not Changed (0.641126)

FBgn0038257

Senescence marker
protein-3

1.65443

10.

13.6

Not Changed (0.577934)

FBgn0013770

Cysteine proteinase-1

1.65436

17.6

19.2

Not Changed (0.807631)

FBgn0025879

tissue inhibitor of
metalloproteases

1.65058

19.2

19.6

Not Changed (0.744938)

FBgn0034870

CG13559

1.646

9.6

9.2

Not Changed (0.823678)

FBgn0014269

proliferation disrupter

1.64505

15.6

12.8

Not Changed (0.638971)

FBgn0027601

BcDNA:GH02901

1.64319

20.8

19.6

Not Changed (0.877353)

FBgn0034259

CG64591.64219

17.2

18.

Not Changed (0.856405)

FBgn0039678

CG181111.64094

14.8

15.6

Down (0.0912869)

FBgn0035881

CG7176

1.63744

1.6

2.4

Not Changed (0.658178)

FBgn0036876

CG9451

1.63583.6

5.2

Not Changed (0.7904)

FBgn0038525

CG143291.623972.

1.2

Down (0.320034)

FBgn0038738

CG4572

1.62377

17.2

22.4

Not Changed (0.546444)

FBgn0035484

CG11594

1.62141

9.2

11.6

Not Changed (1.26861)

FBgn0036533

CG61511.62038

8.4

6.8

Not Changed (1.15278)

FBgn0038556

CG7321

1.61756

7.6

4.4

Not Changed (1.93357)

FBgn0035445

CG120141.61732

18.4

6.4

Not Changed (0.801971)

FBgn0032494

CG59451.60659

1.2

22.8

Not Changed (0.783012)

FBgn0038749

CG44681.60639

17.6

14.8

Not Changed (1.16876)

FBgn0032844

CG10746

1.60335

19.2

20.4

Not Changed (0.928295)

FBgn0038409

CG68151.60221

18.4

20.4

Not Changed (1.23986)

FBgn0034632

CG15668

1.60144

18.4

21.6

Not Changed (1.0891)

FBgn0036106

CG64091.59712

19.6

19.2

Not Changed (0.676547)

FBgn0037146

CG74701.59466

16.8

20.4

Not Changed (1.12553)

FBgn0003738

Triose phosphate
isomerase

1.59436

10.

8.

Not Changed (1.30312)

FBgn0036619

CG47841.59404

2.8

3.6

Down (0.422368)

FBgn0039338

CG45481.59401

9.6

12.8

Not Changed (1.19963)

Supplemental Information for Ueda et al.
FBgn0034429

CG18607

1.58708

8.4

17.2

Not Changed (0.647681)

FBgn0028647

CG11902

1.58344

10.8

8.

Not Changed (1.01319)

FBgn0032213

CG53901.58308

18.4

19.6

Not Changed (0.839385)

FBgn0026878

EG:22E5.12

1.58016

12.4

16.

Not Changed (0.780674)

FBgn0036572

CG5165

1.57853

9.6

10.4

Not Changed (1.59601)

FBgn0032836

CG10680

1.56876

6.4

1.6

Not Changed (0.51212)

FBgn0010288

Ubiquitin carboxy-terminalhydrolase

1.5671914.8

0.4

Not Changed (1.14789)

FBgn0035726

CG99531.56286

19.2

21.2

Not Changed (1.3658)

FBgn0032729

CG10639

1.56115

11.2

9.6

Not Changed (0.857882)

FBgn0031845

CG9232

1.55565

4.

7.2

Not Changed (0.916696)

FBgn0015622

Calnexin 99A

1.554

17.6

16.

Not Changed (0.981196)

FBgn0033565

CG18003

1.55225

6.4

8.4

Not Changed (1.08237)

FBgn0010621

T-complex Chaperonin 5

1.55122

9.6

16.4

Not Changed (0.735536)

Supplemental Information for Ueda et al.

Table 2: Drosophila Genes Rhythmically Expressed in Light-Dark Condition.
Accession #Gene Name

Correlation(LD)Phase(LD)mRNA Levels in Clk(Clk/wt)

FBgn0030106

CG121200.9888

1.2

Not Changed (0.741749)

FBgn0036289

CG10657

0.984897

18.8

Not Changed (0.598144)

FBgn0035921

CG13305

0.983021

3.2

Down (0.103586)

FBgn0005614

trp-like

0.975107

7.6

Not Changed (1.20046)

FBgn0001263

inactivation no afterpotential D

0.97196

1.6

Not Changed (0.921595)

FBgn0025814

Microsomal glutathione Stransferase-like

0.961461

8.8

Not Changed (0.647979)

FBgn0027604

BcDNA:GH02712

0.960888

20.

Not Changed (0.646978)

FBgn0037977

CG31320.960819

20.

Not Changed (0.526222)

FBgn0036094

CG141530.960559

19.6

Not Changed (0.611659)

FBgn0001624

discs large 1

0.960522

21.2

Not Changed (1.28049)

FBgn0031629

CG32440.955695

19.2

Not Changed (1.46115)

FBgn0037468

CG19430.954076

17.6

Not Changed (0.87738)

FBgn0035499

Chd64

0.949662

2.8

Not Changed (1.14926)

FBgn0039464

CG63300.947241

20.4

Not Changed (1.38855)

FBgn0031436

CG3214

0.946706

20.

Not Changed (1.15067)

FBgn0010218

Calphotin

0.94464

22.4

Up (2.51686)

FBgn0016122

Angiotensin-converting enzymerelated

0.943545

8.8

Not Changed (0.914123)

FBgn0033411

CG8805

0.943186

22.

Not Changed (0.751144)

FBgn0037777

CG117220.942222

20.

Not Changed (0.879737)

FBgn0011746

anachronism

0.94159

17.6

Not Changed (0.551526)

FBgn0032694

CG151620.939453

17.2

Not Changed (1.06215)

FBgn0026619

tafazzin0.935343

19.6

Not Changed (1.0347)

LD44686.3prime-hit

CG15761

0.933106

15.6

Not Changed (0.973325)

FBgn0026616

alpha-Man-IIb

0.93277

22.4

Not Changed (1.79242)

FBgn0005619

Histidine decarboxylase

0.930556

22.4

Not Changed (1.15452)

FBgn0002936

neither inactivation nor
afterpotential A

0.930496

24.

Not Changed (0.907259)

FBgn0031767

CG91310.929797

19.6

Not Changed (0.69664)

FBgn0033523

CG12895

0.929786

21.2

Not Changed (0.715952)

Supplemental Information for Ueda et al.

FBgn0003888

betaTubulin6D

0.928946

8.8

Not Changed (1.24992)

FBgn0035961

CG49480.928059

13.6

Not Changed (0.596847)

FBgn0000489

cAMP-dependent protein
kinase0.927351

16.

Not Changed (0.862854)

FBgn0025725

alpha-coatomer protein

0.924793

8.4

Not Changed (0.847149)

FBgn0038519

CG5826

0.923895

22.4

Not Changed (0.720366)

FBgn0040594

CG11957

0.923862

8.4

Not Changed (1.58088)

LD37921.3prime-hit

EST mapped to
FBgn0032812(CG10263) and
FBgn0032811(CG10268)

0.923399

6.8

Down (0.297359)

LP11484.3prime-hit

Epidermal growth factor
receptor

0.922569

8.

Not Changed (0.967832)

LD8195.3prime-hit

CG3981

0.922121

20.

Not Changed (1.41938)

FBgn0034579

CG93530.921983

20.

Not Changed (0.720687)

FBgn0030769

CG130120.919985

8.

Not Changed (0.858997)

FBgn0031925

Cyp4d210.919672

17.2

Not Changed (0.705324)

FBgn0032159

CG58850.919279

8.8

Not Changed (1.16854)

FBgn0032451

CG12292

0.918993

10.

Not Changed (1.32118)

FBgn0004784

inactivation no afterpotential C

0.917874

3.6

Not Changed (1.84412)

FBgn0003091

Protein C kinase 53E

0.917581

22.4

Not Changed (1.49291)

FBgn0032514

CG93020.914038

10.8

Not Changed (0.997264)

FBgn0031215

CG11450

0.91391

11.2

Not Changed (1.39138)

FBgn0033189

CG21400.9132

6.8

Not Changed (0.761967)

FBgn0033311

CG86430.912517

13.6

Not Changed (1.03754)

FBgn0033218

CG13830.912291

10.4

Not Changed (1.03467)

FBgn0031684

CG86800.911988

20.4

Not Changed (0.937254)

FBgn0040588

CG138410.911142

3.2

Up (3.37187)

FBgn0038305

CG65720.910951

21.6

Not Changed (0.804201)

FBgn0036462

CG17166

0.910045

20.

Not Changed (0.581676)

FBgn0013272

Metallothionein A promoter
construct of Fashena

0.909927

18.4

Not Changed (0.791062)

FBgn0034443

CG10460

0.908479

20.

Not Changed (0.966422)

FBgn0033198

CG20800.908124

3.6

Not Changed (1.41531)

FBgn0036157

CG75600.908122

8.8

Not Changed (1.28688)

Supplemental Information for Ueda et al.

FBgn0036834

CG68360.907185

1.2

Not Changed (0.746597)

FBgn0004511

dusky

0.906651

14.4

Not Changed (0.506098)

FBgn0003031

polyA-binding protein

0.90578

6.4

Not Changed (0.872431)

FBgn0030572

CG144130.905711

20.8

Not Changed (0.957716)

FBgn0036928

CG76540.905641

21.2

Not Changed (0.906804)

FBgn0039208

CG66430.905591

8.4

Not Changed (1.51549)

FBgn0025839

EG:152A3.7

0.904707

21.2

Not Changed (1.30516)

FBgn0031999

CG84190.904439

20.

Not Changed (1.24126)

FBgn0014002

Protein disulfide isomerase

0.904222

6.8

Not Changed (0.976589)

FBgn0036661

CG97050.904179

12.8

Not Changed (0.83109)

FBgn0000579

Enolase0.903988

9.2

Not Changed (1.28223)

GH28833.3prime-hit

CG26400.903512

19.6

Not Changed (0.707981)

FBgn0030967

CG72820.903193

9.6

Not Changed (1.13245)

FBgn0030245

CG16370.901396

21.2

Not Changed (0.761693)

FBgn0037892

CG52420.901039

21.6

Not Changed (0.77375)

FBgn0033944

CG101270.900895

22.8

Not Changed (1.19234)

FBgn0022344

CG103400.900446

20.8

Not Changed (1.08002)

FBgn0032349

CG47790.900267

6.

Not Changed (1.30951)

FBgn0025885

myo-inositol-1-phosphatesynthase

0.899938

11.6

Not Changed (0.982148)

FBgn0000527

ebony

0.899251

23.2

Not Changed (0.953041)

FBgn0004919

goliath

0.898116

14.4

Not Changed (1.28279)

FBgn0037697

CG93630.89795

2.

Not Changed (1.61043)

FBgn0033899

CG130160.897744

11.2

Not Changed (0.845761)

FBgn0032775

CG175440.896862

19.2

Not Changed (0.923974)

FBgn0033356

CG82290.896284

0.4

Not Changed (1.16418)

GH188.3prime-hit

CG10732

0.895403

9.6

Up (2.01194)

FBgn0000153

black

0.89512

16.4

Not Changed (0.649156)

FBgn0011674

inscuteable

0.894469

18.8

Down (0.385713)

FBgn0036681

CG13027

0.893135

6.8

Not Changed (1.53048)

FBgn0034343

CG17534

0.891727

6.8

Not Changed (0.608243)

FBgn0014868

Oligosaccharyltransferase
48kD subunit

0.890837

10.

Not Changed (1.11327)

Supplemental Information for Ueda et al.

SD7726.3prime-hit

CG32290.890694

18.

Down (0.393495)

FBgn0032266

CG183020.890397

16.4

Not Changed (0.736976)

FBgn0037159

CG114710.890215

18.4

Not Changed (0.722335)

FBgn0037344

CG29260.88962

7.6

Not Changed (1.44363)

FBgn0040751

CG130180.88863

19.6

Not Changed (0.747751)

FBgn0037127

CG14566

0.888257

9.6

Not Changed (0.601657)

FBgn0004655

wings apart-like

0.887844

8.4

Not Changed (1.82101)

FBgn0039414

CG14557

0.887103

13.6

Not Changed (0.688497)

FBgn0010638

Sec61beta

0.88709

8.4

Not Changed (0.953869)

FBgn0035467

CG10790.887063

20.4

Not Changed (0.85724)

FBgn0020412

JIL-1

0.886928

15.2

Not Changed (1.16865)

GH2872.3prime-hit

CG41440.88666

0.4

Not Changed (1.15616)

FBgn0015011

Adenosylhomocysteinase 89E

0.886309

10.4

Not Changed (1.08343)

FBgn0038220

CG122070.885986

14.

Not Changed (1.00828)

FBgn0019940

Rhodopsin 6

0.885602

10.8

Not Changed (0.60671)

FBgn0031038

CG142080.885507

16.4

Not Changed (1.08093)

FBgn0027610

BcDNA:GH02431

0.884726

22.

Not Changed (0.987823)

FBgn0033249

CG11191

0.884

7.2

Not Changed (0.805721)

FBgn0033232

CG12159

0.883912

8.

Not Changed (0.801779)

FBgn0011016

Signal sequence receptor beta

0.883896

8.

Not Changed (0.90539)

FBgn0033039

CG78970.882986

17.6

Not Changed (1.10957)

FBgn0003074

Phosphoglucose isomerase

0.882903

9.6

Not Changed (0.981852)

FBgn0038996

CG69490.882643

18.

Not Changed (0.945061)

FBgn0000241

brown

0.882362

15.6

Not Changed (0.839488)

FBgn0037648

CG11975

0.881781

21.2

Not Changed (1.25997)

FBgn0032512

CG93050.881549

20.

Not Changed (1.20646)

FBgn0032205

CG49570.880829

19.6

Not Changed (0.910368)

FBgn0030743

CG99210.880802

19.6

Not Changed (0.554965)

FBgn0011336

Oligosaccharyl transferase 3

0.880394

9.2

Not Changed (1.13719)

FBgn0036816

CG39790.880284

22.8

Not Changed (1.08762)

FBgn0035046

CG36830.880121

20.

Not Changed (1.12581)

FBgn0020386

Protein kinase 61C

0.879943

10.4

Not Changed (0.945787)

Supplemental Information for Ueda et al.

FBgn0036824

CG39020.879356

3.6

Not Changed (0.656566)

FBgn0038474

CG51840.879232

20.8

Not Changed (0.922567)

FBgn0033981

Cyp6a210.878532

22.4

Not Changed (0.773527)

FBgn0037117

CG112480.878061

12.

Not Changed (1.02485)

FBgn0034179

CG68050.877542

23.6

Not Changed (1.07319)

FBgn0012044

BTB-protein-II

0.877529

24.

Not Changed (1.1759)

FBgn0039745

CG79500.877124

16.

Not Changed (0.575186)

FBgn0038160

CG97590.877072

9.6

Down (0.341763)

FBgn0038617

CG12333

0.877001

19.6

Not Changed (1.58132)

FBgn0035744

CG86280.876736

10.

Not Changed (0.730261)

FBgn0037672

CG12952

0.876153

10.

Not Changed (1.06704)

FBgn0031801

CG94980.874937

8.4

Not Changed (0.909373)

FBgn0039653

CG14580.874911

22.

Not Changed (0.705733)

FBgn0037845

CG14694

0.873926

9.2

Not Changed (0.906723)

FBgn0030817

CG49910.873643

19.6

Not Changed (1.05815)

LD1981.3prime-hit

amphiphysin

0.873414

20.8

Not Changed (1.20236)

FBgn0027528

BcDNA:LD21405

0.873319

19.2

Not Changed (0.989338)

FBgn0030013

CG15830.873164

8.8

Not Changed (1.4524)

FBgn0031819

CG95390.872091

8.4

Not Changed (1.07493)

FBgn0029820

CG167210.872021

18.4

Not Changed (1.1983)

FBgn0034576

CG93500.871891

21.2

Not Changed (1.33783)

FBgn0032666

CG57580.871724

2.4

Up (3.2)

FBgn0036372

CG10083

0.871333

18.4

Not Changed (0.988226)

FBgn0039178

CG6356

0.871265

5.2

Not Changed (1.11908)

FBgn0038149

CG97960.870853

18.8

Not Changed (0.688749)

FBgn0037241

CG146460.870498

14.8

Not Changed (0.89259)

FBgn0000675

flipper0.870133

20.

Not Changed (0.599036)

FBgn0035133

Ptpmeg0.869949

2.

Not Changed (1.74558)

FBgn0030480

CG16600.869836

20.4

Not Changed (0.792351)

FBgn0013743

Serotonin receptor 2

0.86982

13.2

Not Changed (0.866807)

FBgn0038141

CG98290.869581

18.8

Not Changed (0.946535)

FBgn0027359

Tim80.869427

20.

Not Changed (0.757241)

Supplemental Information for Ueda et al.

FBgn0029721

CG70100.869184

20.

Not Changed (1.04556)

FBgn0035504

CG15003

0.869152

9.2

Not Changed (0.880692)

FBgn0039644

CG11897

0.868551

13.6

Not Changed (0.898246)

FBgn0032222

CG50370.868443

17.6

Not Changed (0.811767)

FBgn0036371

CG107450.86807

8.4

Not Changed (0.894917)

FBgn0002354

lethal (3) 87Df

0.867929

20.4

Not Changed (1.08643)

FBgn0036182

CG60840.867835

7.2

Not Changed (1.28709)

FBgn0014906

CG34880.867818

15.2

Not Changed (0.930836)

FBgn0033533

CG18379

0.867593

9.2

Not Changed (1.11166)

FBgn0028507

BG:DS09217.4

0.867335

20.4

Not Changed (1.2061)

FBgn0033663

CG89830.866596

10.4

Not Changed (0.910163)

FBgn0033065

Cyp6w10.866576

8.8

Down (0.312898)

FBgn0035318

CG90180.866033

10.8

Not Changed (0.873648)

FBgn0034909

CG47970.866033

7.6

Not Changed (0.610629)

FBgn0035909

CG68220.865611

9.2

Not Changed (0.889946)

FBgn0032342

CG47130.864725

10.

Not Changed (1.28074)

FBgn0037929

CG147140.864662

10.4

Not Changed (1.50447)

FBgn0004597

Cyclin C

0.863679

15.6

Not Changed (0.8358)

FBgn0036288

CG10660

0.863151

16.4

Not Changed (0.72088)

FBgn0032906

CG92730.862869

11.2

Down (0.479725)

FBgn0030558

CG14610.861678

7.6

Not Changed (0.661567)

FBgn0036312

CG17667

0.861134

19.2

Not Changed (0.894136)

FBgn0035656

CG10479

0.860884

15.2

Not Changed (0.809121)

FBgn0015805

Rpd3

0.860766

10.

Not Changed (0.814574)

FBgn0031539

CG88440.860677

21.6

Not Changed (0.832176)

FBgn0035427

CG149590.860114

19.2

Not Changed (0.73742)

FBgn0038818

CG40580.859927

1.6

Not Changed (1.24036)

FBgn0032713

CG173230.859685

21.2

Not Changed (1.32501)

FBgn0023537

EG:171D11.1

0.859634

3.2

Not Changed (1.05569)

FBgn0031590

CG37020.858785

9.6

Not Changed (0.958037)

FBgn0036951

CG70170.858046

18.8

Not Changed (0.731972)

FBgn0037054

CG105230.857663

14.8

Not Changed (0.86489)

Supplemental Information for Ueda et al.

GH1453.3prime-hit

CG111420.857631

3.2

Not Changed (0.944324)

FBgn0037379

CG10979

0.856797

11.2

Not Changed (0.865291)

FBgn0030921

CG62900.856514

22.8

Down (0.447372)

FBgn0000250

cactus

0.856477

20.8

Not Changed (0.845922)

FBgn0032985

CG126280.856098

6.8

Not Changed (0.804096)

FBgn0030974

CG73580.854878

8.8

Not Changed (1.26818)

FBgn0038682

CG58350.854854

10.

Not Changed (1.02493)

FBgn0037757

CG85160.854576

5.2

Not Changed (0.781576)

FBgn0036556

CG58300.854542

9.6

Not Changed (1.214)

FBgn0027606

BcDNA:GH02636

0.853875

8.

Not Changed (1.17229)

FBgn0034976

CG40490.853103

6.8

Not Changed (0.906307)

FBgn0023489

PvuII-PstI homology 13

0.8531

17.6

Not Changed (1.25839)

FBgn0032783

CG102370.852585

17.6

Not Changed (0.735589)

FBgn0002783

moira

0.852498

9.2

Not Changed (0.84733)

FBgn0039024

CG47210.85246

10.8

Not Changed (1.04974)

FBgn0039502

CG59650.851015

8.8

Not Changed (1.43251)

FBgn0036319

CG110100.850989

8.4

Not Changed (0.837816)

FBgn0004055

unzipped

0.850356

17.2

Not Changed (0.803668)

FBgn0030610

CG90650.849489

19.6

Not Changed (0.760141)

FBgn0003249

Rhodopsin 3

0.849318

4.4

Not Changed (1.25852)

FBgn0037978

CG35710.848928

1.6

Not Changed (1.12545)

FBgn0040693

CG13799

0.848924

20.8

Down (0.240425)

FBgn0029648

CG36030.848226

16.4

Not Changed (0.817772)

FBgn0022349

CG19100.848095

8.8

Not Changed (0.972999)

FBgn0037111

CG14576

0.848001

9.6

Down (0.270514)

FBgn0011673

Myosin 31DF

0.847852

8.8

Not Changed (1.15813)

FBgn0001128

Glycerol 3 phosphate
dehydrogenase

0.847422

8.

Not Changed (0.79992)

FBgn0028479

BcDNA:GH12558

0.84733

7.6

Not Changed (0.566172)

FBgn0032164

CG45880.847055

20.4

Down (0.494961)

FBgn0014184

gut feeling

0.846375

4.8

Not Changed (1.21304)

FBgn0029545

CG116420.846225

6.4

Not Changed (0.789411)

Supplemental Information for Ueda et al.

FBgn0004456

multiple edematous wings

0.845501

9.6

Not Changed (1.26838)

FBgn0029762

CG32520.845331

7.6

Not Changed (0.888971)

FBgn0034643

CG103210.845059

21.6

Not Changed (1.34611)

FBgn0028698

Rho-kinase

0.844632

10.8

Not Changed (0.946048)

FBgn0034605

CG156610.844562

4.

Not Changed (0.551974)

FBgn0034436

CG119610.84449

11.2

Not Changed (0.686442)

FBgn0038000

CG100140.844249

14.8

Not Changed (0.805754)

FBgn0037906

CG14704

0.843776

8.8

Not Changed (0.677468)

FBgn0029896

CG31680.843337

12.

Not Changed (1.43122)

FBgn0028582

liquid facets

0.842441

2.4

Not Changed (1.75644)

FBgn0037114

CG71600.841945

3.6

Not Changed (0.607901)

FBgn0033208

CG15770.841389

18.8

Not Changed (1.08562)

FBgn0035840

CG75280.839941

18.8

Not Changed (0.947682)

FBgn0030143

CG121410.839873

22.4

Not Changed (0.920032)

FBgn0031049

CG142140.839565

8.4

Not Changed (0.801914)

FBgn0033100

CG34200.839065

20.

Not Changed (0.695677)

FBgn0011296

lethal (2) essential for life

0.838814

9.6

Not Changed (1.47595)

FBgn0032134

CG38640.838536

3.6

Not Changed (1.14483)

FBgn0003471

beta Spectrin

0.838503

6.8

Not Changed (1.2449)

FBgn0037044

CG105850.8385

16.4

Not Changed (0.837197)

FBgn0030968

CG73220.838064

9.6

Not Changed (0.850436)

FBgn0033717

CG88390.837941

8.4

Not Changed (1.10646)

FBgn0031380

CG42330.837755

7.6

Not Changed (1.33519)

FBgn0030115

CG15797

0.837333

13.2

Not Changed (1.22346)

FBgn0033638

CG90050.83726

18.8

Not Changed (0.633449)

FBgn0038437

CG14898

0.837126

18.4

Not Changed (1.22529)

FBgn0040850

CG152100.836736

18.

Not Changed (0.537483)

FBgn0036435

CG50310.836481

10.8

Not Changed (1.60861)

FBgn0032032

CG17294

0.836396

1.6

Up (3.26507)

FBgn0040734

CG150650.836385

4.8

Not Changed (1.23541)

FBgn0001168

hairy

0.836271

10.8

Not Changed (0.890057)

FBgn0030734

CG99110.836024

9.2

Not Changed (0.95587)

Supplemental Information for Ueda et al.

FBgn0038038

CG51670.83568

8.4

Not Changed (0.840469)

FBgn0038795

CG43350.835205

6.4

Not Changed (1.30877)

FBgn0034634

CG10494

0.834925

20.8

Not Changed (0.819302)

FBgn0032336

CG149190.834912

22.4

Not Changed (1.22836)

FBgn0035723

CG99430.834904

10.8

Not Changed (0.884346)

FBgn0038172

CG96210.834804

20.

Not Changed (1.70577)

FBgn0036020

CG83360.834732

19.6

Not Changed (1.04314)

FBgn0035055

CG38720.834675

18.

Not Changed (0.967525)

FBgn0013725

phyllopod

0.834019

20.8

Not Changed (0.806751)

FBgn0033548

CG76370.833637

20.4

Not Changed (0.63177)

FBgn0033085

CG15908

0.833562

20.4

Not Changed (0.900138)

FBgn0023167

Small ribonucleoprotein Sm D3

0.833526

15.2

Not Changed (0.918318)

FBgn0033259

CG112100.833421

9.2

Not Changed (1.05957)

FBgn0035483

CG11340.832929

12.8

Not Changed (0.791833)

FBgn0038236

Cyp313a1

0.832548

16.

Not Changed (1.18576)

FBgn0029876

CG39600.832459

9.2

Not Changed (1.40607)

FBgn0000114

arrest0.832408

10.4

Not Changed (0.974543)

FBgn0027095

ARP-like

0.832332

7.6

Not Changed (1.14234)

FBgn0030060

CG20040.832155

11.2

Not Changed (1.06033)

FBgn0036901

CG87560.831885

21.6

Not Changed (0.924105)

FBgn0030704

CG159160.831601

20.4

Not Changed (0.746553)

FBgn0034727

CG36330.831333

18.4

Not Changed (1.04298)

FBgn0025352

Thiolase

0.831293

9.2

Not Changed (0.87403)

FBgn0038201

CG99180.831104

20.4

Not Changed (1.54021)

FBgn0039022

CG47250.831069

6.8

Not Changed (0.839101)

FBgn0030767

CG45240.830526

15.6

Not Changed (1.02451)

FBgn0036146

CG141410.829921

19.6

Not Changed (1.17445)

FBgn0037277

CG17735

0.829908

10.4

Not Changed (1.47714)

FBgn0034245

CG144820.829592

20.8

Not Changed (1.10584)

FBgn0024978

EG:95B7.3

0.829466

24.

Not Changed (0.944852)

FBgn0036762

CG74300.829159

22.

Not Changed (1.29082)

FBgn0031408

CG108820.828549

8.4

Not Changed (1.02928)

Supplemental Information for Ueda et al.

FBgn0039064

CG44670.82846

6.4

Not Changed (0.676126)

FBgn0027785

NP15.60.828424

20.

Not Changed (1.12289)

FBgn0031260

CG118400.827925

7.6

Not Changed (1.93671)

FBgn0037528

CG10409

0.827854

16.8

Not Changed (0.913988)

FBgn0011361

mitochondrial acyl carrier
protein 1

0.826931

20.8

Not Changed (1.15404)

FBgn0035940

CG50120.82673

22.

Not Changed (0.867359)

FBgn0031417

CG35970.826537

8.8

Not Changed (1.25577)

FBgn0034474

CG13873

0.82638

20.4

Not Changed (0.921361)

FBgn0033784

CG133220.826019

11.6

Not Changed (0.652718)

FBgn0039756

CG97430.8259785.2

Not Changed (0.710164)

FBgn0040551

CG11686

0.825751

3.6

Not Changed (1.18429)

FBgn0010235

Kinesin light chain

0.825314

17.2

Not Changed (0.973826)

FBgn0032900

CG14401

0.824836

15.2

Not Changed (0.987616)

FBgn0023395

Chd3

0.824747

12.

Not Changed (1.31257)

FBgn0032322

CG167430.824375

4.4

Not Changed (0.586805)

FBgn0033502

CG129100.824149

12.8

Not Changed (1.19988)

FBgn0032606

CG17932

0.824047

20.4

Down (0.284543)

FBgn0013467

igloo

0.823002

18.8

Not Changed (1.22575)

FBgn0024832

AP-50

0.822931

20.

Not Changed (1.32818)

FBgn0035181

CG92050.822873

3.2

Not Changed (1.19769)

FBgn0000715

FMRFamide-related

0.822247

3.2

Not Changed (1.45619)

FBgn0014141

cheerio0.822238

11.6

Not Changed (1.75625)

FBgn0032877

CG26170.82217

9.2

Not Changed (0.858738)

FBgn0034949

CG17263

0.822097

9.2

Not Changed (0.800954)

FBgn0035806

CG74960.822002

11.6

Down (0.39001)

FBgn0005648

Pabp2

0.821969

7.2

Not Changed (0.840513)

FBgn0038875

CG60560.821445

22.4

Not Changed (1.20882)

FBgn0030183

CG15309

0.821437

21.6

Not Changed (1.39141)

FBgn0036891

CG93720.82129

4.4

Not Changed (0.766233)

FBgn0033797

CG133280.821078

20.

Not Changed (0.943512)

FBgn0011604

Imitation SWI

0.821071

8.

Down (0.44077)

Supplemental Information for Ueda et al.

FBgn0030796

CG48290.820718

18.8

Not Changed (1.10845)

FBgn0034091

CG84480.820696

16.8

Not Changed (1.15893)

FBgn0038678

CG142830.820638

20.4

Not Changed (1.14491)

FBgn0039586

CG184360.82063

9.6

Not Changed (1.0355)

FBgn0039350

CG173830.820545

22.8

Not Changed (1.02919)

FBgn0004580

Calbindin 53E

0.820079

23.2

Not Changed (0.601)

FBgn0033519

CG11825

0.819808

13.6

Not Changed (0.557463)

FBgn0033131

CG128420.819797

24.

Not Changed (0.749488)

FBgn0033324

CG147440.819709

17.6

Not Changed (0.987532)

FBgn0029615

CG14047

0.819393

7.6

Not Changed (1.27029)

FBgn0026630

nessy

0.819015

23.2

Not Changed (0.913815)

LD224.3prime-hit

Neurotactin

0.819013

7.6

Not Changed (1.05565)

FBgn0036547

CG17032

0.818807

9.6

Not Changed (0.825397)

FBgn0000054

Adh transcription factor 1

0.818707

10.

Not Changed (0.850464)

FBgn0023407

Saccharomyces cerevisiae
UAS construct a of Sotillos

0.81858

22.4

Not Changed (0.886797)

FBgn0034698

CG66980.818245

8.4

Not Changed (0.864327)

LD22520.3prime-hit

EST mapped to
FBgn0002638(Bj1) and
FBgn0000079(Amy-p)0.818185

18.8

Not Changed (1.2406)

FBgn0005776

Protein phosphatase 2A at 29B

0.817884

22.4

Not Changed (1.08512)

FBgn0031024

CG12233

0.817561

20.4

Not Changed (0.800908)

FBgn0036511

CG64980.817549

4.8

Not Changed (1.3591)

FBgn0031069

CG12703

0.817473

11.2

Not Changed (0.80104)

FBgn0004777

Ccp84Ag

0.817418

21.6

Not Changed (1.76315)

FBgn0040799

CG13051

0.816937

21.6

Not Changed (1.16694)

FBgn0032720

CG10603

0.816358

19.2

Not Changed (0.91928)

FBgn0029620

CG79810.816307

19.6

Up (2.16575)

FBgn0027499

BcDNA:LD26050

0.816038

18.4

Not Changed (1.20622)

FBgn0015621

Clipper

0.815885

5.2

Not Changed (0.578973)

FBgn0037315

CG16708

0.815505

10.8

Not Changed (1.13453)

HL1868.3prime-hit

CG10077

0.815287

12.

Not Changed (1.97693)

FBgn0017429

CG59890.815013

19.2

Not Changed (0.957181)

Supplemental Information for Ueda et al.

FBgn0027565

BcDNA:GH08385

0.814908

20.4

Not Changed (1.29825)

FBgn0032160

CG45980.814753

10.8

Not Changed (0.506154)

FBgn0033588

CG132280.814019

4.4

Not Changed (1.06178)

FBgn0039623

CG19510.813733

15.6

Not Changed (1.13021)

FBgn0030184

CG29680.813712

20.4

Not Changed (1.09383)

FBgn0032263

CG74000.8137

12.

Not Changed (0.836588)

FBgn0036857

CG96290.813515

9.2

Not Changed (1.05962)

FBgn0033245

CG87230.813402

9.6

Not Changed (0.868462)

FBgn0028741

EG:52C10.5

0.813101

16.

Not Changed (1.52548)

FBgn0038347

CG185220.812881

1.2

Not Changed (0.564992)

FBgn0037186

CG11241

0.812561

15.6

Not Changed (0.7515)

FBgn0031064

CG125310.812165

3.2

Not Changed (1.05979)

FBgn0037933

CG14716

0.811733

21.2

Not Changed (1.09946)

FBgn0039703

CG78290.811669

8.8

Up (2.57052)

FBgn0033359

CG82130.811668

10.8

Down (0.416378)

FBgn0040878

CG159110.811533

18.4

Not Changed (1.47819)

FBgn0032469

CG99320.810865

7.2

Not Changed (1.74075)

FBgn0033934

CG173850.810844

4.8

Not Changed (1.06727)

FBgn0005649

Rox8

0.810225

13.2

Not Changed (1.16235)

FBgn0035480

CG149840.810072

3.2

Not Changed (1.22135)

FBgn0036546

CG17033

0.809829

17.6

Not Changed (1.07427)

FBgn0029843

CG58940.80938

11.6

Not Changed (0.671637)

FBgn0028694

Rpn11

0.808808

13.2

Not Changed (0.664207)

FBgn0033095

CG34090.808675

8.8

Not Changed (1.57499)

FBgn0036581

CG50570.808025

20.

Not Changed (0.848952)

FBgn0030731

CG34150.807769

9.2

Not Changed (0.940837)

FBgn0036585

CG130710.807599

20.8

Up (2.08237)

FBgn0038612

CG76760.807515

20.

Not Changed (1.79033)

FBgn0040962

CG15868

0.807416

7.6

Not Changed (1.04786)

FBgn0036237

CG185930.807028.

Not Changed (0.667453)

FBgn0031937

CG13795

0.80698.4

Not Changed (1.07253)

GH13437.3prime-hit

CG58890.806859

20.

Not Changed (0.867643)

Supplemental Information for Ueda et al.

FBgn0033329

CG85750.806851

8.4

Not Changed (1.45942)

FBgn0004057

Zwischenferment

0.80682

10.

Not Changed (0.716608)

FBgn0031088

CG153220.806627

2.4

Not Changed (0.761035)

FBgn0034709

CG30740.805989

6.

Not Changed (1.32531)

GH18645.3prime-hit

temperature-induced paralytic
E

0.805653

12.

Not Changed (1.90233)

FBgn0031806

CG95060.805636

16.8

Not Changed (1.23759)

FBgn0037269

CG10550.80561

19.6

Not Changed (1.1074)

FBgn0035111

CG169400.804873

8.

Not Changed (1.032)

FBgn0031773

CG91440.804871

14.8

Not Changed (0.879661)

FBgn0039753

CG13590.804698

20.

Not Changed (0.831683)

FBgn0033949

CG101310.80454

10.

Not Changed (0.940996)

FBgn0036645

CG182180.804428

18.8

Not Changed (0.745428)

FBgn0030093

CG70550.804185

12.

Not Changed (0.967508)

FBgn0027919

BcDNA:GM04682

0.804162

7.6

Not Changed (0.785005)

FBgn0031813

CG95270.803989

5.6

Not Changed (1.14009)

FBgn0035423

CG177370.803902

20.4

Not Changed (0.990222)

FBgn0035473

maggie0.803886

20.8

Not Changed (0.592809)

FBgn0030311

CG11699

0.803776

20.

Not Changed (0.904797)

FBgn0035646

CG10487

0.803706

4.4

Not Changed (0.903134)

FBgn0035334

CG89930.803612

20.8

Not Changed (1.0418)

FBgn0031515

CG96640.803533

11.6

Not Changed (0.850805)

FBgn0025676

CKII-alpha subunit interactor-3

0.803506

19.2

Down (0.315254)

FBgn0032238

CG52510.80337

8.4

Not Changed (0.776432)

FBgn0027912

BcDNA:GM12291

0.803183

7.2

Not Changed (1.0067)

FBgn0033466

CG121300.802908

9.6

Not Changed (1.83062)

FBgn0036926

CG76460.802822

21.2

Not Changed (1.13482)

FBgn0038405

CG89270.802746

23.6

Not Changed (0.762008)

FBgn0035471

CG108490.802554

12.8

Not Changed (0.757519)

FBgn0035966

CG46840.802526

7.2

Not Changed (1.27439)

FBgn0037550

CG96670.802412

12.

Down (0.453762)

FBgn0037108

CG11306

0.801726

14.4

Not Changed (0.946048)

Supplemental Information for Ueda et al.

FBgn0001942

Eukaryotic initiation factor 4a(middle region of transcript)

0.801441

4.8

Not Changed (0.920225)

FBgn0033721

CG131590.80143

17.6

Not Changed (1.04204)

FBgn0038789

CG156850.801253

13.2

Not Changed (0.773353)

FBgn0015276

Protein-L-isoaspartate (Daspartate) O-methyltransferase

0.801076

6.

Not Changed (0.708699)

FBgn0030380

CG182560.801028

9.6

Down (0.440395)

FBgn0039625

CG145170.800748

10.4

Not Changed (0.996068)

FBgn0030828

CG51620.800738

11.6

Not Changed (1.20534)

FBgn0037371

CG20970.800699

4.4

Not Changed (1.17734)

FBgn0040846

CG174960.800681

7.2

Not Changed (0.753265)

FBgn0020513

ade50.800376

10.

Not Changed (1.4366)

FBgn0003250

Rhodopsin 40.800204

4.4

Not Changed (0.904268)

FBgn0032864

CG24930.800049

9.6

Not Changed (0.716315)

FBgn0031936

CG13794

0.799825

10.4

Not Changed (0.555661)

FBgn0025630

EG:22E5.3

0.799803

12.4

Not Changed (0.9865)

FBgn0031228

CG11455

0.799678

21.6

Not Changed (1.62593)

FBgn0035278

CG12023

0.799633

3.6

Not Changed (0.513892)

FBgn0038665

CG12269

0.799512

22.

Not Changed (0.744644)

FBgn0010220

DEAD box protein 45A

0.799399

22.4

Not Changed (1.22953)

FBgn0036101

CG64490.79921

10.

Not Changed (1.3714)

FBgn0030292

CG11752

0.798808

21.6

Not Changed (0.946495)

FBgn0032340

CG6181

0.798529

9.2

Not Changed (1.20068)

FBgn0038925

CG6022

0.798295

20.4

Not Changed (0.973265)

FBgn0037793

CG39530.798007

22.8

Not Changed (1.35561)

FBgn0035673

CG6602

0.797795

12.4

Not Changed (0.639905)

FBgn0039293

CG118510.797785

16.

Not Changed (0.635268)

FBgn0026415

Imaginal Disc Growth Factor 4

0.797535

4.4

Not Changed (1.24075)

FBgn0034356

CG10924

0.79723

21.6

Down (0.00170775)

FBgn0032513

CG65650.796972

20.

Not Changed (0.984242)

FBgn0033071

CG8324

0.796826

6.4

Not Changed (0.693478)

FBgn0026872

EG:80H7.10

0.796591

22.4

Not Changed (0.954048)

FBgn0003691

thread

0.796579

20.4

Not Changed (1.05349)

Supplemental Information for Ueda et al.

FBgn0037217

CG14636

0.796065

20.8

Not Changed (0.640948)

FBgn0039635

CG11876

0.795704

20.

Not Changed (1.15085)

FBgn0016672

Inositol polyphosphate 1phosphatase0.795362

7.6

Not Changed (0.955502)

FBgn0030782

CG18358

0.795096

4.8

Not Changed (1.33727)

FBgn0033000

CG144640.794586

19.2

Not Changed (0.840349)

FBgn0033918

CG85310.794537

14.8

Not Changed (0.955616)

FBgn0030576

CG158900.794395

8.

Not Changed (0.898768)

FBgn0035076

CG101420.794376

21.2

Down (0.456167)

FBgn0000473

Cytochrome P45-6a2

0.79408

9.2

Not Changed (0.837222)

FBgn0035795

CG16998

0.793954

22.

Not Changed (0.617987)

FBgn0027547

BcDNA:GH11112

0.793529

21.2

Not Changed (0.784249)

FBgn0036043

CG81770.793502

6.8

Not Changed (0.762211)

FBgn0036303

CG10753

0.793358

8.8

Not Changed (0.733876)

FBgn0034142

CG8306

0.793237

16.4

Not Changed (0.717751)

FBgn0004363

porin

0.79316

4.8

Not Changed (1.02087)

FBgn0029639

CG144190.792975

12.

Down (0.423226)

FBgn0027657

globin 1

0.792757

21.6

Not Changed (0.912639)

FBgn0033875

CG63570.792711

20.

Up (2.00526)

FBgn0029972

CG1422

0.792507

8.4

Not Changed (1.44212)

FBgn0030672

CG9281

0.792217

8.

Not Changed (0.772432)

FBgn0029888

CG3192

0.792145

19.6

Not Changed (1.10954)

FBgn0004611

Phospholipase C at 21C

0.791669

5.2

Not Changed (1.76061)

FBgn0034428

CG18606

0.791421

10.4

Not Changed (1.17024)

FBgn0038799

CG42880.791328

24.

Not Changed (1.67824)

FBgn0032135

CG38810.790946

22.

Not Changed (1.24012)

FBgn0030001

CG15335

0.790451

14.4

Not Changed (0.831689)

FBgn0015509

lin-19-like

0.790297

16.4

Not Changed (1.28135)

FBgn0034051

Myelodysplasia/myeloid
leukemia factor

0.790296

20.8

Not Changed (0.957546)

FBgn0030510

CG12177

0.790223

21.6

Not Changed (0.723716)

FBgn0039216

CG136210.789985

18.4

Not Changed (0.870577)

FBgn0030213

CG15298

0.789848

6.8

Not Changed (0.90723)

Supplemental Information for Ueda et al.

FBgn0022268

KDEL receptor

0.789614

9.6

Not Changed (0.700072)

FBgn0004512

Multi drug resistance 49

0.789344

1.2

Up (2.43509)

FBgn0003886

alphaTubulin85E

0.789304

11.6

Not Changed (1.21663)

FBgn0037638

CG83790.789273

18.

Down (0.332462)

FBgn0033654

CG8991

0.788444

11.6

Not Changed (1.11896)

FBgn0033881

CG133450.78841

17.6

Not Changed (0.982622)

FBgn0034588

CG93940.788049

21.6

Not Changed (0.579216)

FBgn0030451

CG157170.787743

8.4

Not Changed (0.517254)

FBgn0028469

BcDNA:LD28120

0.787693

10.4

Not Changed (0.600034)

FBgn0002174

lethal (2) tumorous imaginaldiscs

0.787348

20.4

Not Changed (0.984768)

LD27203.3prime-hit

EST mapped to
FBgn0034212(CG6564) and
FBgn0034211(CG15901)

0.787179

18.4

Not Changed (0.617882)

FBgn0039737

CG79200.787073

3.2

Not Changed (0.962605)

FBgn0035528

CG150120.787036

11.6

Not Changed (0.878078)

FBgn0036870

CG14095

0.786219

15.2

Down (0.205065)

FBgn0031800

CG9497

0.786197

23.6

Not Changed (1.41485)

FBgn0038010

CG18158

0.78606

9.2

Not Changed (0.808324)

FBgn0030766

CG45210.785915

15.6

Not Changed (1.76502)

FBgn0014340

males absent on the first

0.785611

22.8

Not Changed (0.907364)

FBgn0020383

RasGap0.785431

9.6

Not Changed (1.06498)

FBgn0024986

EG:132E8.3

0.784411

20.

Not Changed (1.02705)

FBgn0032899

CG93380.784352

20.4

Not Changed (1.14229)

FBgn0034855

CG98890.783991

17.6

Not Changed (0.773748)

FBgn0003887

betaTubulin56D

0.783695

11.2

Not Changed (0.732308)

FBgn0023479

Tequila

0.78353

6.

Not Changed (1.00887)

FBgn0030201

CG28830.783003

18.

Not Changed (1.15252)

FBgn0026753

Vacuolar H+ ATPase G-subunit

0.782865

19.6

Not Changed (0.715765)

FBgn0035070

CG36500.782723

6.8

Down (0.146379)

FBgn0040534

CG11985

0.782649

19.6

Not Changed (0.878596)

LD12453.3prime-hit

EST mapped to
FBgn0033804(CG4037) and
FBgn0033803(CG4055)

0.782362

24.

Not Changed (1.20602)

Supplemental Information for Ueda et al.

FBgn0032482

CG55470.781749

15.2

Not Changed (0.86173)

FBgn0032084

CG13101

0.781664

23.2

Not Changed (0.983803)

FBgn0020907

Sarcoplasmic calcium-binding
protein 2

0.781448

22.4

Not Changed (0.889177)

FBgn0029626

CG17437

0.781147

11.6

Not Changed (1.05266)

FBgn0039056

centaurin beta 1A

0.781028

10.4

Not Changed (1.03411)

FBgn0032926

CG92430.780995

18.4

Not Changed (0.788269)

FBgn0000083

Annexin IX

0.78075

6.4

Not Changed (1.1602)

FBgn0035808

SP25230.780746

3.2

Up (3.6458)

FBgn0001098

Glutamate dehydrogenase

0.780725

23.2

Not Changed (1.01269)

FBgn0037010

CG48250.779946

19.2

Not Changed (0.784968)

FBgn0039176

CG136100.779877

7.6

Not Changed (0.787843)

FBgn0031172

CG17040.77924

21.2

Not Changed (1.00049)

FBgn0035271

CG20210.779178

18.8

Not Changed (1.03098)

FBgn0037288

CG14661

0.778949

23.2

Not Changed (1.1597)

FBgn0034438

CG9416

0.778836

10.

Not Changed (1.50704)

FBgn0031491

CG172230.778817

3.2

Not Changed (1.12902)

FBgn0036920

CG80040.778684

20.8

Not Changed (0.689589)

FBgn0031362

CG17646

0.778288

24.

Not Changed (0.787003)

FBgn0035314

CG57070.778149

9.2

Not Changed (0.821907)

FBgn0035595

CG10668

0.7781052.8

Down (0.0074996)

FBgn0038413

CG67250.777631

12.8

Not Changed (1.72009)

FBgn0002069

Aspartyl-tRNA synthetase0.777442

8.

Not Changed (0.968428)

FBgn0033073

bicoid-interacting protein 30.777015

2.4

Not Changed (1.63818)

FBgn0036826

CG38930.776943

18.8

Not Changed (0.581938)

FBgn0030977

CG12527

0.776724

12.4

Not Changed (0.802018)

FBgn0036927

CG74330.776369

22.4

Not Changed (1.24305)

FBgn0040575

CG159220.776313

19.6

Not Changed (0.88587)

FBgn0034848

CG98720.776279

9.2

Not Changed (1.02878)

FBgn0004889

twins

0.776274

12.

Not Changed (1.09173)

FBgn0024980

EG:95B7.1

0.776238

2.

Not Changed (1.39642)

FBgn0037066

CG77520.776125

10.

Not Changed (0.664124)

Supplemental Information for Ueda et al.

FBgn0038707

CG72370.77609

3.2

Not Changed (1.52123)

FBgn0040736

CG168440.775905

3.6

Not Changed (1.31632)

FBgn0032726

CG106210.775685

10.8

Up (2.65155)

FBgn0036257

CG68110.775636

18.8

Not Changed (0.867936)

FBgn0002306

stranded at second

0.775551

2.4

Not Changed (1.11072)

FBgn0035680

CG10733

0.77472

8.

Not Changed (1.08872)

FBgn0035292

CG123610.774656

5.6

Not Changed (0.794424)

FBgn0037533

CG27910.774577

5.2

Not Changed (1.12075)

FBgn0020261

pacman0.774248

10.4

Not Changed (1.05039)

FBgn0030160

CG96910.774124

4.4

Not Changed (1.07527)

FBgn0035395

CG149540.773716

6.4

Not Changed (0.97113)

FBgn0034033

CG82040.773629

19.6

Not Changed (0.896595)

FBgn0000206

bride of sevenless

0.773543

0.8

Not Changed (1.32707)

FBgn0037718

CG8286

0.773432

7.6

Not Changed (0.934125)

FBgn0025628

EG:22E5.5

0.773317

11.2

Not Changed (0.81582)

FBgn0030612

CG55990.773026

8.

Not Changed (1.16215)

FBgn0038297

CG4196

0.77302

19.2

Not Changed (1.06374)

FBgn0030512

CG99400.77265

14.8

Not Changed (0.963185)

FBgn0032601

yellow-b

0.772408

21.2

Not Changed (0.94786)

FBgn0001233

Heat shock protein 83

0.772116

7.2

Not Changed (0.961246)

FBgn0031933

CG70680.772071

10.8

Not Changed (1.71364)

FBgn0032076

CG95100.771837

10.4

Not Changed (1.56131)

FBgn0024947

NTPase0.771648

17.6

Not Changed (1.12592)

FBgn0033162

CG17070.77163

10.

Not Changed (0.597547)

FBgn0030552

CG15871

0.771574

20.

Not Changed (0.79077)

FBgn0040602

CG145450.771509

8.

Down (0.334151)

FBgn0031651

CG88490.771063

20.

Not Changed (0.997517)

FBgn0023143

Ubiquitin activating enzyme 10.770945

10.4

Not Changed (0.627095)

FBgn0032633

CG68600.77067

5.6

Not Changed (0.875732)

FBgn0030087

CG77660.770208

6.4

Not Changed (1.08462)

FBgn0030306

CG17510.770023

9.6

Not Changed (0.997467)

FBgn0032854

CG100760.770006

4.4

Not Changed (1.10643)

Supplemental Information for Ueda et al.

FBgn0034602

CG15658

0.769817

19.2

Not Changed (0.528744)

FBgn0034337

CG17524

0.769402

4.

Not Changed (0.527102)

FBgn0038096

CG73400.769067

12.4

Not Changed (1.00023)

FBgn0034951

CG38600.769

20.

Not Changed (0.901201)

FBgn0034812

CG30370.768977

17.6

Not Changed (1.35507)

FBgn0034887

CG54280.768958

23.6

Not Changed (1.1499)

FBgn0037900

CG5276

0.768822

12.4

Not Changed (0.930868)

FBgn0001941

infertile crescent

0.768672

16.8

Not Changed (0.810241)

FBgn0040786

CG14104

0.76866

21.2

Down (0.29409)

FBgn0033253

CG87150.768449

11.2

Not Changed (1.1336)

FBgn0027556

BcDNA:GH10120

0.768144

3.6

Not Changed (1.56678)

FBgn0005585

Calreticulin

0.767943

6.8

Not Changed (0.96947)

FBgn0033321

CG87380.767881

10.8

Not Changed (0.801418)

FBgn0036116

CG78880.76769

22.8

Not Changed (1.51516)

FBgn0039484

CG61240.767681

6.8

Not Changed (0.717314)

FBgn0037089

CG71930.76766

8.8

Not Changed (1.09264)

FBgn0031429

CG153930.767269

20.4

Not Changed (1.05597)

FBgn0033932

CG84220.767032

0.4

Not Changed (1.04199)

FBgn0036726

CG76030.766994

21.2

Not Changed (0.935374)

FBgn0016917

Signal-transducer and activatorof transcription protein at 92E

0.766921

10.4

Not Changed (1.09934)

FBgn0013432

bcn92

0.766896

23.2

Not Changed (0.893153)

FBgn0039220

CG13633

0.766563

0.8

Not Changed (0.916845)

FBgn0030315

CG15191

0.766545

15.2

Not Changed (0.779932)

FBgn0034184

CG9646

0.766482

10.8

Not Changed (1.39882)

FBgn0026749

Yippee0.766375

17.2

Not Changed (1.26961)

FBgn0032426

CG15493

0.76616

21.6

Not Changed (1.92281)

FBgn0004698

mutagen-sensitive 21

0.766154

20.

Not Changed (0.88085)

FBgn0033961

CG12859

0.765534

20.8

Not Changed (1.21079)

FBgn0037896

CG67280.765328

23.6

Not Changed (1.64175)

FBgn0030271

CG152020.764877

18.4

Not Changed (1.01383)

FBgn0030550

CG14050.764857

21.6

Not Changed (0.854241)

Supplemental Information for Ueda et al.

FBgn0032262

CG73840.764785

10.

Not Changed (1.1749)

FBgn0019925

Surfeit 4

0.764685

12.

Not Changed (0.846268)

FBgn0022787

Helicase 89B

0.764562

6.8

Not Changed (1.06596)

FBgn0039938

CG111530.764503

10.

Not Changed (0.900232)

LD28427.3prime-hit

EST mapped to
FBgn0024326(Mkk4) and
FBgn0000447(Dhod)

0.764

15.6

Down (0.153062)

FBgn0038164

CG94120.763534

10.

Not Changed (0.972507)

FBgn0029537

CG14633

0.763266

6.8

Not Changed (0.930736)

FBgn0039496

CG6001

0.76304

4.

Not Changed (1.0727)

FBgn0038823

CG17837

0.762969

20.8

Not Changed (0.726122)

Supplemental Information for Ueda et al.

Table 3: Drosophila Genes Rhythmically Expressed in Constant Dark Condition.
Accession #Gene Name

Correlation(DD)Phase(DD)mRNA Levels in Clk(Clk/wt)

FBgn0034997

CG3376

0.973078

21.6

Not Changed (0.635211)

FBgn0014019

Rhodopsin 5

0.959384

20.

Not Changed (1.72489)

FBgn0004780

Ccp84Ad

0.952131

4.4

Not Changed (1.10431)

FBgn0030041

CG12116

0.946845

4.8

Not Changed (0.978994)

FBgn0013981

Histone H4 replacement

0.942907

18.

Not Changed (1.08651)

FBgn0033593

CG90800.938923

20.

Not Changed (0.578511)

FBgn0040972

CG16978

0.928852

8.

Not Changed (1.49522)

FBgn0034010

CG81570.928276

20.8

Down (0.431862)

FBgn0032197

CG56940.924608

24.

Not Changed (1.22068)

FBgn0034405

CG151020.923839

23.2

Not Changed (0.946224)

FBgn0003495

spatzle0.919219

8.

Not Changed (0.671232)

FBgn0035401

CG12910.919023

1.6

Not Changed (0.90538)

FBgn0031105

CG11738

0.91897

0.4

Not Changed (0.50426)

FBgn0039218

CG136280.916848

4.

Not Changed (0.86316)

FBgn0031189

CG14618

0.916194

18.4

Not Changed (0.984301)

FBgn0001092

Glyceraldehyde 3 phosphate
dehydrogenase 2(3 prime
region of transcript)

0.914812

9.2

Not Changed (1.22912)

LD22726.complete-hit

BG:DS04929.3

0.914308

4.4

Not Changed (1.00564)

FBgn0032773

CG158250.910682

24.

Not Changed (0.607017)

FBgn0037476

CG146110.909874

7.2

Not Changed (0.742651)

FBgn0030425

CG37750.909269

20.8

Down (0.416503)

FBgn0039696

CG78370.905011

6.8

Not Changed (1.06966)

FBgn0014469

Cytochrome P45-4e2

0.904851

21.2

Down (0.464658)

FBgn0038771

CG43900.902746

7.2

Not Changed (0.875122)

FBgn0034341

CG175310.901785

23.2

Down (0.469624)

FBgn0040902

CG27660.901042

23.2

Not Changed (1.06437)

FBgn0033227

CG15480.89908

18.

Not Changed (0.971402)

FBgn0036032

CG167110.896703

5.6

Not Changed (1.37986)

FBgn0030963

CG71010.895603

8.4

Not Changed (1.36695)

Supplemental Information for Ueda et al.

FBgn0032809

CG13078

0.894235

3.6

Not Changed (1.13172)

FBgn0034404

CG15101

0.892912

22.8

Down (0.454531)

FBgn0015287

Replication-factor-C 4kD
subunit

0.889101

13.2

Not Changed (1.00016)

FBgn0037909

CG125930.888692

12.

Not Changed (1.02374)

FBgn0038407

CG61260.887028

22.

Not Changed (0.689865)

FBgn0027348

bubblegum

0.886657

5.2

Not Changed (0.80244)

FBgn0033903

CG83230.885093

4.

Not Changed (0.931351)

FBgn0031456

CG28480.884793

2.8

Not Changed (0.904029)

FBgn0011695

Ejaculatory bulb protein III

0.884515

19.6

Not Changed (1.11683)

FBgn0037387

CG12130.88119

22.4

Not Changed (0.892942)

FBgn0036277

CG104180.880041

17.2

Not Changed (1.05616)

FBgn0001091

Glyceraldehyde 3 phosphate
dehydrogenase 1

0.879763

10.4

Not Changed (1.01442)

FBgn0037926

CG10535

0.879466

19.6

Not Changed (0.938111)

FBgn0036657

CG96970.879309

12.8

Not Changed (1.37291)

FBgn0038147

CG14375

0.878836

15.2

Not Changed (0.866729)

FBgn0030222

CG98060.878556

8.4

Not Changed (1.00358)

FBgn0040590

CG13826

0.87805

13.6

Not Changed (1.57264)

FBgn0034888

CG54310.877301

18.

Not Changed (0.706629)

FBgn0037925

CG17309

0.877203

24.

Not Changed (1.11504)

FBgn0000667

alpha actinin

0.876117

7.2

Not Changed (1.62771)

FBgn0027583

BcDNA:GH06026

0.872941

22.4

Not Changed (0.968589)

FBgn0033269

CG87090.8726

21.2

Not Changed (1.14307)

FBgn0034818

CG135370.86782

4.4

Not Changed (1.20259)

FBgn0033968

CG10200

0.867775

6.

Not Changed (0.724024)

FBgn0035880

CG17352

0.866924

20.4

Down (0.27546)

FBgn0032099

CG95850.866466

6.4

Up (2.4756)

FBgn0032591

CG13261

0.866226

6.4

Not Changed (1.32506)

FBgn0038590

CG123200.865567

16.8

Not Changed (1.0043)

GH15485.3prime-hit

CG17762

0.863796

4.

Not Changed (1.55314)

FBgn0015623

Cytochrome P45 reductase

0.863676

23.2

Not Changed (0.761998)

FBgn0030717

CG89310.863363

1.2

Not Changed (1.26266)Supplemental Information for Ueda et al.

FBgn0011603

inebriated0.863179

5.6

Not Changed (0.652296)

FBgn0029794

CG31380.861405

2.

Not Changed (0.899659)

FBgn0004855

RNA polymerase II 15kD
subunit

0.860417

15.2

Not Changed (0.999371)

FBgn0039118

CG102080.860161

21.6

Not Changed (0.708013)

FBgn0030079

CG72670.859601

0.4

Not Changed (1.37309)

FBgn0026438

Excitatory amino acidtransporter 2

0.858422

23.2

Not Changed (1.11518)

FBgn0013576

heat shock promoter
construct of Stowers

0.858236

2.

Not Changed (1.22444)

FBgn0027844

Carbonic anhydrase 1

0.858232

21.2

Not Changed (0.669501)

FBgn0032085

CG95550.857142

13.2

Not Changed (0.786192)

FBgn0032961

CG14160.856018

0.8

Not Changed (0.538937)

FBgn0031589

CG37140.852443

4.4

Up (2.94007)

FBgn0038419

CG14879

0.852141

21.6

Not Changed (0.764843)

FBgn0032402

CG149450.852006

12.

Up (2.13695)

FBgn0005278

Minute (2) 21AB

0.849638

20.4

Not Changed (0.928402)

FBgn0026387

Odorant receptor 46b

0.849151

3.2

Not Changed (0.885795)

FBgn0036347

CG112810.848662

8.4

Not Changed (0.777881)

FBgn0039526

CG56920.847966

8.4

Not Changed (1.12721)

FBgn0037189

CG144490.846881

10.4

Not Changed (1.06437)

FBgn0031453

CG98940.84648

15.6

Not Changed (1.38597)

FBgn0033962

CG10153

0.846296

3.6

Not Changed (0.952619)

FBgn0033489

CG34590.845733

0.8

Not Changed (1.49877)

FBgn0033544

CG72200.845684

21.2

Not Changed (0.941674)

FBgn0038171

RPE55

0.845647

4.4

Not Changed (1.56378)

FBgn0038304

CG122410.844585

22.8

Not Changed (0.842936)

FBgn0037684

CG81290.844574

22.8

Not Changed (1.7099)

FBgn0005198

gigas

0.843921

4.

Not Changed (1.38498)

FBgn0031942

CG72030.842866

3.6

Not Changed (0.973846)

FBgn0035083

CG28030.840848

0.8

Not Changed (1.13965)

FBgn0024897

b6

0.84084

1.2

Not Changed (1.28906)

FBgn0031948

CG71490.840406

0.4

Not Changed (1.37249)

Supplemental Information for Ueda et al.

FBgn0003134

Protein phosphatase 1alphaat 96A

0.840354

19.2

Not Changed (0.877062)

FBgn0034564

CG93440.840268

12.4

Not Changed (0.819967)

FBgn0033612

CG132100.839469

14.8

Not Changed (0.790936)

FBgn0038321

CG62180.839333

0.4

Not Changed (1.16807)

FBgn0024939

Ribosomal protein L8

0.838699

17.6

Not Changed (1.09293)

FBgn0013726

peanut0.838247

4.8

Not Changed (0.946407)

FBgn0030737

CG99140.837857

10.8

Up (3.51872)

FBgn0036863

CG96700.83768

18.

Not Changed (0.974338)

FBgn0033746

CG13153

0.837451

4.

Not Changed (1.17334)

FBgn0037764

CG94590.837291

16.4

Not Changed (0.772493)

FBgn0031145

CG17400.836876

14.8

Not Changed (0.934764)

FBgn0031896

CG45020.836204

12.

Not Changed (1.35767)

FBgn0029522

CG13373

0.835847

12.4

Not Changed (1.34459)

FBgn0037467

CG11040.835123

17.2

Not Changed (0.726636)

FBgn0037537

CG27670.834981

0.8

Not Changed (1.4381)

FBgn0033814

CG46700.834406

14.4

Not Changed (1.44492)

FBgn0038194

Cyp6d50.83421

19.6

Not Changed (1.15827)

FBgn0004885

tolkin0.834147

20.4

Not Changed (0.908193)

FBgn0030701

CG16952

0.8334

5.2

Not Changed (1.06025)

FBgn0038111

CG12360

0.833242

16.

Not Changed (1.11352)

FBgn0038022

CG4381

0.832626

1.6

Not Changed (0.600297)

FBgn0030423

CG18453

0.832109

21.6

Not Changed (0.718705)

FBgn0031897

CG137840.832053

23.6

Not Changed (1.43047)

FBgn0035270

CG13933

0.831879

11.2

Not Changed (1.52169)

FBgn0032403

CG123170.831619

17.6

Not Changed (0.970787)

FBgn0039672

CG19060.831427

4.4

Not Changed (1.27405)

FBgn0031645

CG30360.830976

23.6

Not Changed (0.88862)

FBgn0033398

CG20490.830899

17.6

Not Changed (1.52959)

FBgn0038357

CG56230.830824

12.8

Up (4.08674)

FBgn0032323

CG60930.830606

10.8

Not Changed (1.92119)

FBgn0038878

CG33010.830361

8.8

Not Changed (1.06366)Supplemental Information for Ueda et al.

FBgn0031263

CG27890.829538

1.6

Not Changed (0.926468)

FBgn0031418

CG36090.828503

12.4

Not Changed (0.688517)

FBgn0038462

CG17556

0.82784

8.4

Not Changed (1.32437)

FBgn0038805

CG42170.827778

15.6

Not Changed (0.945294)

FBgn0035296

CG118140.827756

3.2

Not Changed (0.81649)

FBgn0033805

CG40620.827662

23.6

Not Changed (1.83595)

FBgn0027567

BcDNA:GH07921

0.826927

24.

Not Changed (1.08063)

FBgn0032681

CG102830.826131

22.4

Not Changed (0.939026)

FBgn0029588

CG14798

0.826035

22.8

Not Changed (1.14374)

FBgn0033562

CG67510.825989

21.2

Not Changed (0.832886)

FBgn0034851

CG11079

0.82573

10.8

Up (2.88794)

GH15539.3prime-hit

Protein tyrosine phosphatase
4E

0.825545

22.8

Not Changed (0.705514)

FBgn0015788

Rab-related protein 1

0.824886

20.8

Not Changed (0.999635)

FBgn0037653

CG119820.824551

6.

Not Changed (0.839259)

FBgn0035197

CG91300.823958

15.2

Not Changed (1.01938)

FBgn0034394

CG15096

0.823874

23.2

Not Changed (0.77221)

FBgn0039115

CG102140.822851

20.4

Not Changed (0.955817)

FBgn0031389

CG42590.822636

20.4

Down (0.354375)

FBgn0032400

CG67700.822075

22.

Not Changed (1.02709)

FBgn0011327

Ubiquitin C-terminalhydrolase

0.822011

10.8

Not Changed (0.821561)

FBgn0039931

CG110910.821227

8.

Not Changed (0.926711)

FBgn0039656

CG119510.820884

4.8

Down (0.288498)

FBgn0030834

CG86750.820729

17.2

Not Changed (0.853952)

FBgn0040993

CG173250.820724

5.6

Not Changed (1.82619)

FBgn0030026

CG109640.820341

24.

Not Changed (0.847895)

FBgn0040827

CG133150.820091

16.

Not Changed (1.08916)

FBgn0040931

CG90340.82006

16.

Not Changed (0.856957)

FBgn0035013

CG135800.819697

10.

Not Changed (1.11615)

FBgn0038037

Cyp9f20.818758

23.2

Not Changed (1.06086)

FBgn0032162

CG45920.818649

13.6

Not Changed (0.627709)

FBgn0032904

CG93420.818526

14.8

Not Changed (0.839055)

Supplemental Information for Ueda et al.

FBgn0013263

Trithorax-like

0.818112

3.2

Not Changed (0.689646)

SD02875.3prime-hit

Vacuolar H+ ATPase 16kD
subunit

0.817878

19.2

Not Changed (0.726146)

FBgn0033657

CG82710.817662

4.8

Down (0.481255)

FBgn0033835

CG18279

0.817465

22.8

Up (2.00779)

FBgn0031657

CG37560.816953

4.

Not Changed (1.19915)

FBgn0003447

singed

0.816204

21.6

Not Changed (0.919273)

FBgn0038573

CG79130.815706

4.

Not Changed (0.943133)

FBgn0030542

CG124810.815686

19.6

Down (0.332016)

FBgn0031399

CG70740.815125

23.2

Not Changed (1.10187)

FBgn0038981

CG53460.814991

3.6

Not Changed (0.818062)

FBgn0037106

CG113070.814891

13.2

Not Changed (1.09022)

FBgn0038535

CG182120.813996

12.8

Not Changed (1.26899)

FBgn0037234

CG97950.813738

15.2

Not Changed (0.847769)

FBgn0030446

CG21900.813702

14.4

Not Changed (0.660296)

FBgn0035943

CG56530.813525

15.6

Up (3.45413)

FBgn0031871

CG10158

0.813512

13.6

Not Changed (0.584122)

FBgn0026429

gamma-tubulin ring protein 91

0.813259

6.

Not Changed (1.0888)

FBgn0032299

CG17127

0.812942

23.2

Not Changed (0.735391)

FBgn0038339

CG61180.812643

8.

Not Changed (0.529198)

FBgn0039253

CG62380.812618

7.2

Not Changed (0.875152)

FBgn0040871

CG12479

0.8123

6.8

Not Changed (1.39714)

FBgn0037292

CG20220.81229

5.2

Not Changed (1.9927)

FBgn0001142

Glutamine synthetase 1

0.812115

15.6

Not Changed (1.54112)

FBgn0038306

CG65630.811942

15.2

Not Changed (0.66844)

FBgn0036022

CG83290.811017

19.2

Not Changed (0.957881)

FBgn0037788

CG39400.810837

9.6

Not Changed (1.29858)

LD32106.3prime-hit

EST mapped to
FBgn0036008(CG3408) and
FBgn0010408(RpS9)

0.810642

19.2

Up (2.99359)

FBgn0030447

CG22000.810405

10.8

Not Changed (0.835245)

FBgn0037548

CG79000.81012

19.6

Up (4.1138)

FBgn0038872

CG58740.809946

22.4

Not Changed (0.99537)

Supplemental Information for Ueda et al.

FBgn0035851

CG79990.809723

14.8

Not Changed (1.11792)

FBgn0035392

CG12710.809164

19.2

Not Changed (0.73087)

FBgn0039494

CG58960.808557

9.6

Not Changed (0.504433)

FBgn0031221

CG31640.80853

19.2

Not Changed (0.702182)

FBgn0000416

Saposin-related

0.808184

22.8

Not Changed (0.989542)

FBgn0040532

CG83690.808161

18.4

Not Changed (1.08628)

FBgn0033854

CG61520.807825

2.

Not Changed (0.767081)

FBgn0032699

CG10383

0.80777

2.4

Not Changed (0.740033)

FBgn0036270

CG18638

0.807752

3.2

Not Changed (1.16758)

FBgn0038299

CG66870.80773

22.

Not Changed (0.977344)

FBgn0035039

CG36080.807569

14.8

Not Changed (0.839651)

FBgn0013307

Ornithine decarboxylase 1

0.807448

7.2

Not Changed (0.906127)

FBgn0038343

CG148710.80724

3.2

Not Changed (1.08186)

FBgn0030593

CG95120.806896

22.8

Not Changed (1.32485)

FBgn0032467

CG99340.806868

3.2

Not Changed (0.861557)

FBgn0037913

CG67830.806378

11.2

Not Changed (1.03096)

GM686.3prime-hit

CG73690.806253

6.4

Not Changed (1.45529)

FBgn0015568

alpha-Esterase-1

0.805595

0.4

Down (0.395918)

FBgn0040614

CG128820.803861

7.6

Not Changed (0.545733)

FBgn0028918

BG:DS01068.1

0.803393

8.4

Not Changed (0.841634)

FBgn0015513

myoblast city

0.803154

16.8

Not Changed (0.942626)

FBgn0034500

CG11200

0.802848

10.4

Not Changed (0.626345)

FBgn0038109

CG116560.802765

15.2

Down (0.408715)

FBgn0020236

ATP citrate lyase

0.802639

12.

Not Changed (0.687114)

FBgn0038166

CG95880.802592

3.6

Not Changed (0.914578)

FBgn0036302

CG106320.802144

22.8

Not Changed (0.742021)

LD29477.3prime-hit

CG171380.800031

10.4

Not Changed (1.0997)

FBgn0000606

even skipped

0.799931

12.8

Not Changed (0.849444)

FBgn0033557

CG12325

0.799785

22.

Not Changed (0.895876)

FBgn0036314

CG107540.799626

3.2

Not Changed (1.10149)

FBgn0040732

CG16926

0.799258

10.4

Down (0.448041)

FBgn0031865

CG10806

0.798442

7.6

Not Changed (0.529693)

Supplemental Information for Ueda et al.

FBgn0034897

CG11299

0.798066

14.8

Not Changed (0.791813)

FBgn0029544

CG16994

0.798018

5.6

Not Changed (1.01412)

FBgn0028691

Rpn4

0.797923

24.

Not Changed (0.80274)

FBgn0001092

Glyceraldehyde 3 phosphate
dehydrogenase 2(5 prime
region of transcript)

0.797495

8.

Up (2.49185)

FBgn0023000

methuselah

0.79637

18.

Not Changed (1.2607)

FBgn0033125

CG12846

0.795898

22.

Not Changed (0.571452)

FBgn0036663

CG96740.79588

23.2

Not Changed (1.32933)

FBgn0035229

CG78520.795704

2.8

Up (3.1151)

FBgn0036837

CG18135

0.795509

16.

Down (0.489702)

FBgn0010770

peter pan

0.795152

15.2

Not Changed (0.82451)

FBgn0015766

Msr-1100.793851

12.8

Not Changed (1.10527)

FBgn0039565

CG4884

0.793826

17.6

Not Changed (0.67232)

FBgn0035995

CG35290.793236

1.2

Not Changed (0.785187)

FBgn0013756

Bx34

0.793197

6.4

Not Changed (0.97967)

FBgn0034483

CG16894

0.793089

11.6

Not Changed (0.715747)

FBgn0028399

TMS1d0.792762

20.

Not Changed (1.02325)

FBgn0030317

CG1561

0.792416

11.2

Not Changed (0.708132)

FBgn0032398

CG6766

0.791743

23.6

Not Changed (0.86334)

FBgn0037095

CG7184

0.79116

7.2

Not Changed (1.05634)

FBgn0027571

BcDNA:GH07626

0.79095

7.2

Not Changed (0.831247)

FBgn0014073

Tie-like receptor tyrosine
kinase0.790161

0.4

Not Changed (1.00968)

FBgn0030749

Annexin B110.790141

17.6

Not Changed (1.1903)

FBgn0011760

cut up0.789501

22.8

Not Changed (1.30312)

FBgn0035027

CG35110.789319

14.8

Not Changed (1.88666)

FBgn0004876

center divider

0.788803

11.2

Up (3.34025)

FBgn0036283

CG4392

0.788291

20.4

Up (2.27925)

FBgn0033485

CG1381

0.788285

0.4

Not Changed (1.15141)

FBgn0037699

CG81470.788235

4.4

Not Changed (0.631967)

FBgn0033900

CG82570.787632

23.6

Not Changed (0.926932)

FBgn0038914

CG178200.787332

13.2

Not Changed (1.1534)

Supplemental Information for Ueda et al.

FBgn0030883

CG77720.786593

22.4

Not Changed (0.766523)

FBgn0038588

CG7156

0.786102

18.4

Not Changed (0.82633)

FBgn0000150

abnormal wing discs

0.78588

16.4

Not Changed (1.04858)

FBgn0031368

CG12704

0.785588

3.2

Not Changed (1.63252)

FBgn0035389

CG12740.785293

11.2

Down (0.448034)

FBgn0038725

CG61840.785269

7.2

Not Changed (1.48077)

FBgn0029709

CG35640.784965

17.6

Not Changed (0.827657)

FBgn0030173

CG153130.78492

13.6

Not Changed (0.633513)

FBgn0039114

CG10374

0.784771

10.4

Not Changed (0.781277)

FBgn0034048

CG8256

0.784685

9.2

Not Changed (1.13122)

FBgn0033989

CG76390.784564

3.6

Not Changed (1.65778)

FBgn0040609

CG33480.783903

10.4

Down (0.0518378)

FBgn0033988

CG7761

0.783749

3.2

Down (0.440083)

FBgn0037714

CG9396

0.783711

6.8

Not Changed (1.52259)

FBgn0036433

CG96280.783401

7.2

Not Changed (0.984248)

FBgn0040890

CG14199

0.78303

14.8

Not Changed (0.95058)

FBgn0034328

CG15066

0.782785

21.6

Down (0.128703)

FBgn0032214

CG49680.782766

5.6

Not Changed (0.696025)

FBgn0027378

MRG15

0.782307

6.4

Not Changed (1.10884)

FBgn0037761

CG85340.782127

8.8

Not Changed (1.13706)

FBgn0011638

La autoantigen-like

0.782029

22.

Down (0.34108)

FBgn0001108

Glued

0.782002

2.4

Not Changed (1.17585)

FBgn0039743

CG7946

0.781782

20.

Not Changed (0.914369)

FBgn0028946

Odorant receptor 35a

0.781742

9.6

Not Changed (0.915059)

FBgn0030681

CG82310.781571

12.8

Not Changed (0.900145)

FBgn0038421

CG179310.781456

14.4

Not Changed (1.12683)

FBgn0035500

CG14998

0.78142

13.6

Not Changed (0.748155)

FBgn0003231

refractory to sigma P

0.781217

1.6

Not Changed (0.817752)

FBgn0033571

CG11979

0.781194

6.

Not Changed (1.03726)

FBgn0004629

Cystatin-like

0.780822

19.2

Not Changed (1.5299)

FBgn0034953

CG180200.780373

9.2

Not Changed (0.852751)

FBgn0036123

CG63020.780158

1.6

Not Changed (0.989942)

Supplemental Information for Ueda et al.

FBgn0039846

CG11337

0.779853

6.

Not Changed (1.06935)

FBgn0039835

CG122200.779696

18.4

Not Changed (0.885124)

FBgn0031143

CG15320.779497

10.

Not Changed (0.815783)

FBgn0037073

CG73380.779196

22.

Not Changed (0.942615)

FBgn0029906

CG45420.779003

3.2

Not Changed (1.1248)

FBgn0036290

CG10638

0.778849

15.6

Down (0.398665)

FBgn0037309

CG2676

0.778825

12.8

Not Changed (1.81424)

FBgn0032285

CG17108

0.778558

11.2

Not Changed (1.41312)

FBgn0023507

EG:87B1.3

0.77822

6.

Not Changed (1.84299)

FBgn0034584

CG93640.778093

24.

Not Changed (0.969752)

FBgn0032476

CG54390.778086

10.4

Not Changed (1.0676)

FBgn0033338

CG82690.777909

22.8

Not Changed (0.968697)

FBgn0011704

Ribonucleoside diphosphate
reductase small subunit

0.777769

9.6

N.D.

FBgn0030363

CG157360.777686

17.6

Not Changed (0.893939)

FBgn0036517

CG169800.776453

1.2

Not Changed (0.760008)

FBgn0036697

CG77250.775914

6.

Not Changed (0.529161)

FBgn0010416

heat shock construct of
Banga

0.775313

11.2

Not Changed (1.07891)

GH4717.3prime-hit

CG38110.774991

4.

Not Changed (1.43596)

FBgn0034762

CG135150.774981

12.

Not Changed (0.677972)

GH04205.3prime-hit

EST mapped to
FBgn0038749(CG4468) and
FBgn0038748(CG12378)

0.774851

21.6

Not Changed (0.883047)

FBgn0039917

CG99050.77466

16.4

Not Changed (1.57343)

FBgn0037936

CG69080.774654

22.

Not Changed (0.894006)

FBgn0039875

CG19370.774515

0.4

Not Changed (0.716815)

FBgn0000242

Beadex0.77383

12.8

Not Changed (0.871129)

FBgn0032246

CG51680.773319

10.4

Not Changed (1.0135)

FBgn0033837

CG17034

0.773174

2.4

Not Changed (1.4434)

FBgn0030897

CG57440.77305

2.4

Not Changed (1.60894)

FBgn0037676

CG88610.772473

6.4

Not Changed (1.38139)

FBgn0038563

CG77800.772038

21.6

Not Changed (0.505361)

FBgn0027580

BcDNA:GH06348

0.771959

4.4

Not Changed (0.735164)

Supplemental Information for Ueda et al.

FBgn0038074

CG61880.771942

21.6

Not Changed (1.05572)

FBgn0033800

CG4016

0.771931

21.2

Not Changed (1.27662)

FBgn0031605

CG15438

0.77193

19.2

Not Changed (0.97493)

FBgn0034046

CG82530.771526

20.4

Down (0.464903)

FBgn0032155

CG45390.771425

14.8

Not Changed (0.650997)

FBgn0003317

saxophone

0.771398

7.2

Not Changed (0.92914)

LD45776.3prime-hit

CG9126

0.771366

22.4

Not Changed (1.04174)

FBgn0039538

CG12883

0.771124

23.6

Not Changed (1.06137)

FBgn0001092

Glyceraldehyde 3 phosphate
dehydrogenase 2(middle
region of transcript)

0.771018

8.4

Not Changed (1.46543)

FBgn0031493

CG36050.770599

16.8

Not Changed (1.50126)

FBgn0026414

Kaz1

0.769979

0.4

Not Changed (1.5539)

FBgn0019650

twin of eyeless0.76999.6

Not Changed (0.933142)

FBgn0037874

CG48000.769684

10.8

Not Changed (1.09885)

FBgn0040823

CG14162

0.769678

5.2

Not Changed (0.922601)

FBgn0030540

CG115810.769053

12.8

Not Changed (1.37033)

FBgn0028536

BG:DS00810.3

0.768907

17.2

Not Changed (0.939787)

FBgn0015298

Signal recognition particle
protein 19

0.768395

14.8

Not Changed (1.20012)

FBgn0035060

CG16932

0.768293

23.2

Not Changed (0.862682)

FBgn0031290

CG42760.767879

10.4

Not Changed (1.49703)

FBgn0032114

CG37520.767696

5.2

Not Changed (1.47385)

FBgn0030729

CG125070.767561

13.2

Not Changed (1.14423)

FBgn0038420

CG103110.76693

8.4

Not Changed (1.04736)

FBgn0011661

Moesin-like

0.766816

18.

Not Changed (0.846695)

FBgn0031124

CG13790.766549

10.8

Not Changed (0.756784)

FBgn0025864

Calmodulin-binding protein
related to a Rab3 GDP/GTP
exchange protein

0.766454

18.

Not Changed (0.94504)

FBgn0030456

CG43320.766229

2.

Not Changed (0.978823)

FBgn0038338

CG5166

0.765934

4.

Not Changed (1.50107)

FBgn0012034

Acetyl Coenzyme A synthase

0.765871

9.2

Not Changed (0.721255)

FBgn0023178

Pigment-dispersing factor

0.765658

22.8

Not Changed (0.778467)

Supplemental Information for Ueda et al.

FBgn0030234

CG152110.765387

0.4

Not Changed (0.989739)

FBgn0036864

CG140900.76528

16.4

Not Changed (0.940102)

FBgn0033387

CG80080.765092

17.6

Not Changed (0.560978)

FBgn0000139

absent, small, or homeotic
discs 20.76497

22.4

Not Changed (1.04421)

FBgn0039643

CG11886

0.764948

4.4

Not Changed (0.938265)

FBgn0030996

CG14194

0.764461

3.6

Not Changed (1.36787)

FBgn0029800

CG15929

0.763595

7.2

Not Changed (0.737703)

Supplemental Information for Ueda et al.

Table 4: Rhythmic Biological Processes in Light-Dark Condition.
Categories are defined in the Gene Ontology database and downloaded on March 21, 2001.
Accession #Gene NameClass

Phase (LD)lipid metabolism
Genes in Categories = 79; Cycling Genes = 16; P-value = 5.58025
FBgn0011693

Photoreceptor dehydrogenase

I

2.8

FBgn0004611

Phospholipase C at 21C

II

5.2

FBgn0039756

CG9743II

5.2

FBgn0036182

CG6084II

7.2

FBgn0028479

BcDNA:GH12558

II

7.6

FBgn0030731

CG3415II

9.2

FBgn0025352

ThiolaseII

9.2

FBgn0033245

CG8723II

9.6

FBgn0030968

CG7322II

9.6

FBgn0035744

CG8628II

10.

FBgn0032160

CG4598II

10.8

FBgn0032482

CG5547II

15.2

FBgn0029648

CG3603II

16.4

FBgn0034812

CG3037II

17.6

FBgn0032513

CG6565

II

20.

FBgn0011361

mitochondrial acyl carrier protein 1

II

20.8

circadian rhythm
Genes in Categories = 7; Cycling Genes = 4; P-value = 3.63911
FBgn0023076

Clock

I

2.

FBgn0025680

cryptochrome

I

5.2

FBgn0003068

periodI

13.6

FBgn0014396

timelessI

14.8

Supplemental Information for Ueda et al.

phototransduction
Genes in Categories = 20; Cycling Genes = 6; P-value = 3.38197
FBgn0001263

inactivation no afterpotential D

II

1.6

FBgn0004784

inactivation no afterpotential C

II

3.6

FBgn0003249

Rhodopsin 3

II

4.4

FBgn0003250

Rhodopsin 4

II

4.4

FBgn0019940

Rhodopsin 6

II

10.8

FBgn0002936

neither inactivation nor afterpotential A

II

24.

cytoplasm organization and biogenesis
Genes in Categories = 21; Cycling Genes = 5; P-value = 2.4075
FBgn0030734

CG9911

II

9.2

FBgn0025352

ThiolaseII

9.2

FBgn0032514

CG9302II

10.8

FBgn0024986

EG:132E8.3

II

20.

FBgn0035334

CG8993II

20.8

protein folding
Genes in Categories = 72; Cycling Genes = 10; P-value = 2.38612
FBgn0014002

Protein disulfide isomerase

II

6.8

FBgn0030734

CG9911

II

9.2

FBgn0010621

T-complex Chaperonin 5I

9.6

FBgn0033663

CG8983II

10.4

FBgn0032514

CG9302II

10.8

FBgn0033918

CG8531II

14.8

FBgn0028741

EG:52C10.5

II

16.

FBgn0034091

CG8448II

16.8

FBgn0024986

EG:132E8.3

II

20.

FBgn0002174

lethal (2) tumorous imaginal discs

II

20.4

Supplemental Information for Ueda et al.

metabolism
Genes in Categories = 156; Cycling Genes = 16; P-value = 2.11378
FBgn0023537

EG:171D11.1

II

3.2

LD224.3prime-hit

Neurotactin

II

7.6

FBgn0031380

CG4233II

7.6

FBgn0033065

Cyp6w1II

8.8

FBgn0036857

CG9629II

9.2

FBgn0000473

Cytochrome P45-6a2

II

9.2

FBgn0032340

CG6181

II

9.2

FBgn0031515

CG9664II

11.6

FBgn0000241

brown

II

15.6

FBgn0032167

CG5853I

16.

FBgn0038236

Cyp313a1

II

16.

FBgn0031925

Cyp4d21II

17.2

FBgn0039084

CG10175

I

17.6

FBgn0010383

Cytochrome P45-18a1

I

17.6

FBgn0033981

Cyp6a21II

22.4

FBgn0015714

Cyp6a17I

23.6

amino acid and derivative metabolism
Genes in Categories = 79; Cycling Genes = 10; P-value = 2.09867
FBgn0035881

CG7176I

1.6

LD224.3prime-hit

Neurotactin

II

7.6

FBgn0031380

CG4233II

7.6

FBgn0036157

CG7560II

8.8

FBgn0032076

CG9510II

10.4

FBgn0000153

black

II

16.4

FBgn0036762

CG7430

II

22.

FBgn0036975

CG5618I

22.

Supplemental Information for Ueda et al.

FBgn0005619

Histidine decarboxylase

II

22.4

FBgn0036927

CG7433II

22.4

transport
Genes in Categories = 156; Cycling Genes = 15; P-value = 1.77491
FBgn0039178

CG6356II

5.2

FBgn0036043

CG8177II

6.8

FBgn0034909

CG4797II

7.6

FBgn0029762

CG3252II

7.6

FBgn0039176

CG13610II

7.6

FBgn0031937

CG13795

II

8.4

FBgn0033095

CG3409II

8.8

FBgn0037845

CG14694

II

9.2

FBgn0028469

BcDNA:LD28120

II

10.4

FBgn0029896

CG3168II

12.

SD1469.3prime-hit

CG8468I

13.2

FBgn0034812

CG3037II

17.6

FBgn0026439

Excitatory amino acid transporter 1

I

18.8

FBgn0000527

ebony

II

23.2

FBgn0038799

CG4288II

24.

Supplemental Information for Ueda et al.

Table 5: Rhythmic Biological Processes in Constant Dark Condition.
Categories are defined in the Gene Ontology database and downloaded on March 21, 2001.
Accession #Gene NameClass

Phase (DD)circadian rhythm
Genes in Categories = 7; Cycling Genes = 4; P-value = 4.39497
FBgn0023076

Clock

I

2.

FBgn0025680

cryptochrome

I

5.2

FBgn0003068

periodI

13.6

FBgn0014396

timelessI

15.2

main pathways of carbohydrate metabolism
Genes in Categories = 52; Cycling Genes = 6; P-value = 2.1199
FBgn0035881

CG7176I

2.4

FBgn0027580

BcDNA:GH06348

III

4.4

FBgn0003738

Triose phosphate isomerase

I

8.

FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(5 prime regionof transcript)

III

8.

FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(middle prime
region of transcript)

III

8.4

FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(3 prime regionof transcript)

III

9.2

FBgn0001091

Glyceraldehyde 3 phosphate dehydrogenase 1

III

10.4

FBgn0020236

ATP citrate lyase

III

12.

deubiquitylation
Genes in Categories = 8; Cycling Genes = 2; P-value = 1.56121
FBgn0010288

Ubiquitin carboxy-terminal hydrolase

I

0.4

FBgn0011327

Ubiquitin C-terminal hydrolase

III

10.8

Supplemental Information for Ueda et al.

Table 6: Candidate Molecules Rhythmically Metabolized in Light-Dark Condition.
Information of Enzymes are downloaded on March 21, 2001 from LIGAND metabolic database.
Accession #Gene NameClass

Phase (LD)NAD+
All Related Enzymes= 62; Cycling Enzymes = 16; P-value = 7.11518
FBgn0034390

CG15093I

3.2

FBgn0023537

EG:171D11.1

II

3.2

FBgn0036182

CG6084II

7.2

FBgn0028479

BcDNA:GH12558

II

7.6

FBgn0001128

Glycerol 3 phosphate dehydrogenase

II

8.

FBgn0030731

CG3415II

9.2

FBgn0011768

Formaldehyde dehydrogenase

I

9.6

FBgn0004057

Zwischenferment

II

10.

FBgn0024289

Sorbitol dehydrogenase 1

I

10.4

FBgn0030512

CG9940II

14.8

FBgn0038617

CG12333

II

19.6

FBgn0029888

CG3192II

19.6

FBgn0035046

CG3683

II

20.

FBgn0031024

CG12233

II

20.4

FBgn0036762

CG7430

II

22.

FBgn0001098

Glutamate dehydrogenase

II

23.2

NADH
All Related Enzymes= 60; Cycling Enzymes = 15; P-value = 6.51177
FBgn0034390

CG15093I

3.2

FBgn0023537

EG:171D11.1

II

3.2

FBgn0036182

CG6084II

7.2

FBgn0028479

BcDNA:GH12558

II

7.6

FBgn0001128

Glycerol 3 phosphate dehydrogenase

II

8.

Supplemental Information for Ueda et al.

FBgn0030731

CG3415II

9.2

FBgn0011768

Formaldehyde dehydrogenase

I

9.6

FBgn0004057

Zwischenferment

II

10.

FBgn0024289

Sorbitol dehydrogenase 1

I

10.4

FBgn0038617

CG12333

II

19.6

FBgn0029888

CG3192II

19.6

FBgn0035046

CG3683

II

20.

FBgn0031024

CG12233

II

20.4

FBgn0036762

CG7430

II

22.

FBgn0001098

Glutamate dehydrogenase

II

23.2

CO2
All Related Enzymes= 57; Cycling Enzymes = 14; P-value = 6.01616
FBgn0035881

CG7176I

1.6

FBgn0023537

EG:171D11.1

II

3.2

FBgn0036992

CG11796

I

4.

FBgn0037607

CG8036I

8.8

FBgn0033245

CG8723II

9.6

FBgn0000153

black

II

16.4

FBgn0038617

CG12333

II

19.6

FBgn0039635

CG11876

II

20.

GH13437.3prime-hit

CG5889II

20.

FBgn0029721

CG7010

II20.

FBgn0031024

CG12233

II

20.4

FBgn0034356

CG10924II

21.6

FBgn0036975

CG5618I

22.

FBgn0005619

Histidine decarboxylase

II

22.4

2-Oxoglutarate
All Related Enzymes= 20; Cycling Enzymes = 7; P-value = 4.35145

Supplemental Information for Ueda et al.

FBgn0035881

CG7176I

1.6

FBgn0030558

CG1461

II

7.6

FBgn0031380

CG4233II

7.6

FBgn0038617

CG12333

II

19.6

FBgn0031024

CG12233

II

20.4

FBgn0036927

CG7433II

22.4

FBgn0001098

Glutamate dehydrogenase

II

23.2

NADP+
All Related Enzymes= 28; Cycling Enzymes = 8; P-value = 4.17958
FBgn0035881

CG7176I

1.6

FBgn0036182

CG6084II

7.2

FBgn0030731

CG3415II

9.2

FBgn0030968

CG7322II

9.6

FBgn0004057

Zwischenferment

II

10.

FBgn0037146

CG7470I

16.8

GH13437.3prime-hit

CG5889II

20.

FBgn0001098

Glutamate dehydrogenase

II

23.2

NADPH
All Related Enzymes= 28; Cycling Enzymes = 8; P-value = 4.17958
FBgn0035881

CG7176I

1.6

FBgn0036182

CG6084II

7.2

FBgn0030731

CG3415II

9.2

FBgn0030968

CG7322II

9.6

FBgn0004057

Zwischenferment

II

10.

FBgn0037146

CG7470I

16.8

GH13437.3prime-hit

CG5889II

20.

FBgn0001098

Glutamate dehydrogenase

II

23.2

Supplemental Information for Ueda et al.

L-Glutamate
All Related Enzymes= 30; Cycling Enzymes = 8; P-value = 3.94514
FBgn0030558

CG1461

II

7.6

FBgn0031380

CG4233II

7.6

FBgn0030512

CG9940II

14.8

FBgn0000153

black

II

16.4

FBgn0037146

CG7470I

16.8

FBgn0036975

CG5618I

22.

FBgn0036927

CG7433II

22.4

FBgn0001098

Glutamate dehydrogenase

II

23.2

Protein Cys-Cys
All Related Enzymes= 4; Cycling Enzymes = 3; P-value = 3.26027
FBgn0014002

Protein disulfide isomerase

II

6.8

FBgn0033663

CG8983II

10.4

FBgn0032514

CG9302II

10.8

3-(4-Hydroxyphenyl)pyruvate
All Related Enzymes= 4; Cycling Enzymes = 3; P-value = 3.26027
FBgn0036992

CG11796

I

4.

FBgn0030558

CG1461

II

7.6

FBgn0031380

CG4233II

7.6

4-Aminobutanoate
All Related Enzymes= 4; Cycling Enzymes = 3; P-value = 3.26027
FBgn0000153

black

II

16.4

FBgn0036975

CG5618I

22.

FBgn0036927

CG7433

II

22.4

II

16.4

beta-Alanine
All Related Enzymes= 4; Cycling Enzymes = 3; P-value = 3.26027
FBgn0000153

blackSupplemental Information for Ueda et al.

FBgn0036975

CG5618I

22.

FBgn0036927

CG7433

II

22.4

S-Acetyldihydrolipoamide
All Related Enzymes= 6; Cycling Enzymes = 3; P-value = 2.59581
FBgn0030612

CG5599II

8.

FBgn0039635

CG11876

II

20.

FBgn0029721

CG7010II20.

(1R,2S)-1-Hydroxypropane-1,2,3-tricarboxylate
All Related Enzymes= 6; Cycling Enzymes = 3; P-value = 2.59581
FBgn0035881

CG7176I

1.6

FBgn0038617

CG12333

II

19.6

FBgn0031024

CG12233II

20.4

alpha-D-Glucose 6-phosphate
All Related Enzymes= 2; Cycling Enzymes = 2; P-value = 2.56276
FBgn0036572

CG5165I

9.6

FBgn0003074

Phosphoglucose isomerase

II

9.6

Homogentisate
All Related Enzymes= 2; Cycling Enzymes = 2; P-value = 2.56276
FBgn0036992

CG11796

I

4.

FBgn0032349

CG4779II

6.

2-Methyl-3-oxopropanoate
All Related Enzymes= 2; Cycling Enzymes = 2; P-value = 2.56276
FBgn0034390

CG15093I

3.2

FBgn0023537

EG:171D11.1

II

3.2

(2R)-2-Hydroxy-3-(phosphonooxy)-propanal
All Related Enzymes= 7; Cycling Enzymes = 3; P-value = 2.36995
FBgn0037607

CG8036I

8.8

FBgn0034934

CG2827I

9.6

Supplemental Information for Ueda et al.

FBgn0003738

Triose phosphate isomerase

I

10.

L-Aspartate
All Related Enzymes= 15; Cycling Enzymes = 4; P-value = 2.1941
FBgn0031380

CG4233II

7.6

FBgn0002069

Aspartyl-tRNA synthetase

II

8.

FBgn0000153

black

II

16.4

FBgn0036975

CG5618I

22.

3-Sulfino-L-alanine
All Related Enzymes= 3; Cycling Enzymes = 2; P-value = 2.10102
FBgn0000153

black

II

16.4

FBgn0036975

CG5618I

22.

Hypotaurine
All Related Enzymes= 3; Cycling Enzymes = 2; P-value = 2.10102
FBgn0000153

black

II

16.4

FBgn0036975

CG5618I

22.

Supplemental Information for Ueda et al.

Table 7: Candidate Molecules Rhythmically Metabolized in Contact Dark Condition.
Information of Enzymes are downloaded on March 21, 2001 from LIGAND metabolic database.
Accession #Gene NameClass

Phase (DD)(2R)-2-Hydroxy-3-(phosphonooxy)-propanal
All Related Enzymes = 7; Cycling Enzymes = 5; P-value = 6.08439
FBgn0003738

Triose phosphate isomerase

I

8.

FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(5 prime regionof transcript)

III

8.

FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(middle prime
region of transcript)

III

8.4

FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(3 prime regionof transcript)

III

9.2

FBgn0001091

Glyceraldehyde 3 phosphate dehydrogenase 1

III

10.4

FBgn0034934

CG2827I

10.8

FBgn0037607

CG8036I

12.

D-Glyceraldehyde
All Related Enzymes = 2; Cycling Enzymes = 2; P-value = 2.95013
FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(5 prime regionof transcript)

III

8.

FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(middle prime
region of transcript)

III

8.4

FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(3 prime regionof transcript)

III

9.2

FBgn0001091

Glyceraldehyde 3 phosphate dehydrogenase 1

III

10.4

Thiol
All Related Enzymes = 8; Cycling Enzymes = 3; P-value = 2.73316
FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(5 prime regionof transcript)

III

8.

FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(middle prime
region of transcript)

III

8.4

FBgn0001092

Glyceraldehyde 3 phosphate dehydrogenase 2(3 prime regionof transcript)

III

9.2

FBgn0001091

Glyceraldehyde 3 phosphate dehydrogenase 1

III

10.4

Supplemental Information for Ueda et al.

FBgn0011327

Ubiquitin C-terminal hydrolase

III

10.8

CO2
All Related Enzymes = 57; Cycling Enzymes = 7; P-value = 2.54911
FBgn0036992

CG11796I

1.2

FBgn0035881

CG7176I

2.4

FBgn0013307

Ornithine decarboxylase 1

III

7.2

FBgn0037788

CG3940III

9.6

FBgn0037607

CG8036I

12.

FBgn0033800

CG4016

III

21.2

FBgn0036975

CG5618

I

24.

Arene oxide
All Related Enzymes = 3; Cycling Enzymes = 2; P-value = 2.48279
FBgn0034404

CG15101

III

22.8

FBgn0034405

CG15102III

23.2

Arene diol
All Related Enzymes = 3; Cycling Enzymes = 2; P-value = 2.48279
FBgn0034404

CG15101

III

22.8

FBgn0034405

CG15102III

23.2

GlycolAll Related Enzymes = 3; Cycling Enzymes = 2; P-value = 2.48279
FBgn0034404

CG15101

III

22.8

FBgn0034405

CG15102III

23.2

EpoxideAll Related Enzymes = 3; Cycling Enzymes = 2; P-value = 2.48279
FBgn0034404

CG15101

III

22.8

FBgn0034405

CG15102III

23.2

D-Erythrose 4-phosphate
All Related Enzymes = 4; Cycling Enzymes = 2; P-value = 2.1915

Supplemental Information for Ueda et al.

FBgn0034934

CG2827I

10.8

FBgn0037607

CG8036I

12.

Sedoheptulose 7-phosphate
All Related Enzymes = 5; Cycling Enzymes = 2; P-value = 1.97938
FBgn0034934

CG2827I

10.8

FBgn0037607

CG8036I

12.

CDPAll Related Enzymes = 5; Cycling Enzymes = 2; P-value = 1.97938
FBgn0039846

CG11337

III

6.

FBgn0000150

abnormal wing discs

III

16.4

Supplemental Information for Ueda et al.

Table 8: Drosophila Genes Rhythmically Expressed in Clk Mutants under Light-Dark Condition.
Accession #Gene Name

Correlation(Clk)

Phase(Clk)Class

SD1469.3prime-hit

CG84680.853454

20.4

I

FBgn0033821

CG10799

0.845298

8.

I

FBgn0039309

CG118910.824478

14.

I

FBgn0010288

Ubiquitin carboxy-terminal hydrolase

0.821589

19.6

I

FBgn0039678

CG181110.797167

8.4

I

FBgn0034934

CG28270.785692

9.6

ILD29569.3prime-hit

CG127900.767905

22.

I

FBgn0011296

lethal (2) essential for life

0.894915

1.2

II

FBgn0031590

CG37020.882282

7.6

II

FBgn0033245

CG87230.87222210.

II

FBgn0037533

CG27910.871614

22.4

II

FBgn0033329

CG85750.840156

7.2

II

FBgn0024980

EG:95B7.1

0.824781

18.4

II

FBgn0001098

Glutamate dehydrogenase

0.82167

0.4

II

FBgn0038795

CG43350.791893

9.6

II

FBgn0029648

CG36030.791122

13.2

II

FBgn0035314

CG57070.785339

9.2

II

FBgn0039024

CG47210.780064

20.

II

FBgn0032263

CG74000.776932

6.8

II

FBgn0036901

CG87560.774376

14.

II

FBgn0032775

CG175440.772725

23.2

II

FBgn0039623

CG19510.772627

4.

II

FBgn0025814

Microsomal glutathione S-transferase-like

0.771772

10.4

II

FBgn0039672

CG1906

0.931337

22.4

III

FBgn0039114

CG10374

0.913198

9.2

III

FBgn0038914

CG178200.880089

10.

III

FBgn0037095

CG71840.852037

19.6

III

FBgn0030540

CG115810.828543

6.4

III

FBgn0038299

CG66870.827149

8.4

III

FBgn0039253

CG62380.821042

22.

IIISupplemental Information for Ueda et al.

FBgn0026414

Kaz1

0.815857

10.

III

LD29477.3prime-hit

CG17138

0.805106

7.6

III

FBgn0032961

CG14160.802808

14.8

III

FBgn0032162

CG45920.799051

14.4

III

FBgn0037309

CG2676

0.797918

20.8

III

LD22726.complete-hit

BG:DS04929.3

0.796376

18.4

III

FBgn0038981

CG5346

0.786236

14.4

III

FBgn0025864

Calmodulin-binding protein related to a Rab3
GDP/GTP exchange protein

0.784721

4.8

III

FBgn0035027

CG35110.777969

23.2

III

FBgn0032681

CG102830.777751

22.8

III

FBgn0030447

CG22000.77364

7.2

III

FBgn0012034

Acetyl Coenzyme A synthase

0.77052

10.

III

FBgn0031290

CG42760.767908

20.

III

FBgn0037653

CG11982

0.76414

22.8

IIIGenome-wide Transcriptional Orchestration of Circadian Rhythms inDrosophila
Hiroki R. Ueda, Akira Matsumoto, Miho Kawamura, Masamitsu Iino, Teiichi Tanimura
and Seiichi Hashimoto
J. Biol. Chem. 2002, 277:14048-14052.
doi: 10.1074/jbc.C100765200 originally published online February 19, 2002

Access the most updated version of this article at doi: 10.1074/jbc.C100765200

Click here to choose from all of JBC's e-mail alerts

Supplemental material:
http://www.jbc.org/content/suppl/2002/04/15/277.16.14048.DC1
This article cites 30 references, 12 of which can be accessed free at
http://www.jbc.org/content/277/16/14048.full.html#ref-list-1

Downloaded from http://www.jbc.org/ at University of Tokyo Library on May 29, 2017

Alerts:• When this article is cited• When a correction for this article is posted