BACKGROUND
the development of microarray high-throughput screening platforms for chicken is an important step for gene expression profiling in changes occurring in avian as a response to different challenges and stimuli  <cit> .
the chicken research community uses microarrays for a wide range of applications, including gene expression analysis  <cit> , exon expression analysis  <cit> , novel transcript discovery  <cit> , genotyping  <cit>  and resequencing  <cit> .
in addition, microarray analysis can also be combined with chromatin immunoprecipitation to perform genome-wide identification of transcription factors and their respective binding sites  <cit> .
according to statistics obtained from "gallus expression in situ hybridization analysis" , there is already significant resources constructed for the "whole genome" chicken microarrays.
listed in geisha are: 1) arizona gallus gallus  <dig>  k long oligo array, 2) affymetrix array which cover  <dig>  transcripts corresponding to over  <dig>  chicken genes, 3) fhcrc chicken  <dig> k array, 4) university of delaware-larry cogburn which produced ud_liver_ <dig>  k, ud  <dig>  k metabolic/somatic systems, chicken neuroendocrine system  <dig> k and the del-mar  <dig> k integrated systems and 5) ark genomics which offers a  <dig>  clone chicken embryo array, a  <dig>  cdna chicken immune array, and a  <dig>  clone chicken neuroendocrine array.
gene expression omnibus , publicly accessible through the world wide web at http://www.ncbi.nlm.nih.gov/geo, is a curated public repository for high-throughput gene expression data  <cit> .
platform is one of central data entities of geo which contains a list of probes that define what set of molecules may be detected and can easily be browsed, queried and retrieved to fit user's interests  <cit> .
comprehensive annotation of these arrays will benefit chicken researchers, because they will be able to functionally model their expressed dataset to obtain relevant information about their biological system.
however, most arrays are not associated to any functional information.
the only array that is comprehensively annotated to go is the affymetrix chicken genechip array  <cit> .
this array is the mostly used for gene expression studies as shown in a survey when the chicken research community was polled in july  <dig> http://doodle.com/participation.html?pollid=zwvmhpt5t23tvfv8).
the affymetrix netaffx database links probesets on affymetrix genchip microarrays to go using data from the go consortium  <cit> .
however, the go evidence codes are not linked to any reference that was used to make functional assertions.
this is a challenge to researchers who want to associate their dataset with functional information at the same time showing supporting evidence.
for example, use of an experimental evidence code in a go annotation should be associated with a paper that displays results from a physical characterization of a gene/gene product being annotated.
this allows the researcher to access the detailed information that was used to make the go annotation.
in this study we have re-annotated all gene products associated with probesets on affymetrix chicken genome array using go standards.
however, the go describes normal gene or gene product function  <cit>  such that information about which genes are associated with significant diseases and disorders and which are known to be drug targets is not captured using the go.
this type of information would clearly benefit researchers in modeling diseases.
we therefore used ingenuity pathway analysis to identify significant diseases, disorders, drug targets and types of gene represented on affymetrix chicken genome array.
furthermore, we demonstrate how other microarrays can be annotated using the annotations from affymetrix chicken array.
RESULTS
initial assessment of structural and functional annotation of chicken array
most of chicken arrays currently available are linked to either gene or gene products but very few of the arrays are annotated to any functional information .
the affymetrix chicken array was chosen for this study because it represents most of genomic elements annotated on chicken genome.
initial assessment of annotation of affymetrix chicken genome array are shown .
over 97% of chicken affymetrix probesets are mapped to  <dig>  genes or gene products in total.
other probesets represented on this array are for studying  <dig> different avian viruses.
about 51% of the probesets are associated with go annotations made for  <dig>  genes or gene product.
different chicken arrays  have different gene products represented on them .
column  <dig> &  <dig> shows whether the printed transcripts are linked to a gene , mrna , est or protein.
go in column  <dig> indicates go functional annotation linked to gene products represented on these arrays and evd  indicates evidence code supporting the functional information.
the  or  in columns  <dig> –  <dig> indicates presence or absence of the parameter in that specific column.
+ or - shows that the array is linked or not linked.
*evidence that support the go annotation
functional annotation and go annotation quality
the go annotation of affymetrix chicken probesets does not show any reference supporting the evidence of the annotation as pointed out in methods section.
we re-annotated all gene products represented on this array, regardless of their initial annotations, according to go standards.
we were able to increase the number of go annotations in all three ontologies ; re-annotation increased the total go annotations by 45%, the number of annotated gene products by 10% and the number of probe sets linked to annotated gene products by 13%.
moreover, the quality of the original go annotations in all three go ontologies, as determined by gaq score  <cit> , was improved by the additional annotations .
briefly, the gaq score quantitatively assess the level of detail provided by the go annotation and the type of evidence used to make the annotations.
the overall mean gaq score of all annotations regardless of biological ontology, increased from  <dig> to  <dig>
additional functional information was obtained using the ingenuity pathway analysis  tool to identify the significant biological functions, diseases and disorders that are represented on affymetrix chicken genome array .
the most significant diseases and disorders represented on this array are cancer and genetic disorders, respectively.
cell death was identified to be the most significant molecular and cellular function while organismal survival was the most significant process among the physiological system development.
different types of genes and known drug targets were also identified .
significant biological functions represented on affymetrix chicken genome array.
*based on fisher's exact test p-value ≤  <dig>
tool for array go mapping
improved functional annotation of affymetrix chicken array proved to facilitate the annotation of other arrays, such as the arizona gallus gallus  <dig>  k oligo array v <dig>  .
an array go mapper  tool developed in this study was able to map entrez genes, ensembl genes and genbank accessions from the arizona array to affymetrix annotations in order to retrieve go annotations.
we successfully identified 79% of genes that were common in both arrays , out of which 72% were mapped to go annotations .
the total number of go annotations generated for arizona array was  <dig> .
an example of output generated by agom is shown on additional file  <dig> which includes only the first  <dig>  gene association lines generated for arizona chicken array.
the mean gaq score associated with the go annotations retrieved was  <dig> and was calculated by summing up all gaq scores of all  <dig>  go associations and dividing these by the number of annotated gene products.
these results provide an initial assessment of go annotations available for the arizona chicken array and demonstrates how go annotations can be transferred to identical transcriptional elements represented on multiple arrays.
discussion
the major challenge that faces microarray researchers is interpretation of hundreds of differentially expressed genes into a biologically relevant context.
the gene ontology  consortium provides a controlled vocabulary to annotate the biological knowledge associated with genes or gene products.
in order to make the functional interpretation of microarray dataset less challenging, microarray developers can associate their arrays with functional information.
however, most chicken arrays either have no associated go information or do not follow the go annotation standards  <cit> .
in this study we have re-annotated and improved the go annotation of affymetrix chicken genome array to facilitate annotation of other chicken arrays and microarray experimental datasets.
further, we developed the array go mapper  tool to generate go annotations for chicken arrays with no go information or for microarray experimental datasets and demonstrated its utility by annotating the arizona chicken array which had no associated go information.
by implementing agom researchers will not only obtain functional information for their experimental dataset but will also obtain gaq scores associated with each go term retrieved.
this will help researchers determine the quality of annotations made to their datasets and also help tracking the improvement made by any additional go when there are any updates.
we also provided additional functional information not covered by the go but is associated with the affymetrix chicken genome array.
this additional data broadens the ability of array users to model their datasets, for example infectious disease datasets.
the additional information obtained on diseases, disorders and known drug targets represented on this array will provide light to future research in drug and therapy development.
CONCLUSIONS
improved amount and quality of go annotations of gene products represented on the affymetrix chicken genome array will help researchers to model their genes of interest to high quality functional information by using agom tool.
the existing chicken microarray studies can use agom and this demonstrates how this tool can enhance functional annotation in these studies.
annotation of microarrays of other species will be included in the future.
the top significant diseases and disorders represented on the chicken array correlate well with how the chicken is used as a biomedical model organism to study human diseases and development.
the identified gene types and drug targets allows researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies.

 the development of microarray high-throughput screening platforms for chicken is an important step for gene expression profiling in changes occurring in avian as a response to different challenges and stimuli. the chicken research community uses microarrays for a wide range of applications, including gene expression analysis, exon expression analysis, novel transcript discovery, genotyping and resequencing. in addition, microarray analysis can also be combined with chromatin immunoprecipitation to perform genome-wide identification of transcription factors and their respective binding sites. according to statistics obtained from "gallus expression in situ hybridization analysis", there is already significant resources constructed for the "whole genome" chicken microarrays. listed in geisha are: 1) arizona gallus gallus k long oligo array, 2) affymetrix array which cover transcripts corresponding to over chicken genes, 3) fhcrc chicken k array, 4) university of delaware-larry cogburn which produced ud_liver_ k, ud k metabolic/somatic systems, chicken neuroendocrine system k and the del-mar k integrated systems and 5) ark genomics which offers a clone chicken embryo array, a cdna chicken immune array, and a clone chicken neuroendocrine array. gene expression omnibus, publicly accessible through the world wide web at http://www.ncbi.nlm.nih.gov/geo, is a curated public repository for high-throughput gene expression data. platform is one of central data entities of geo which contains a list of probes that define what set of molecules may be detected and can easily be browsed, queried and retrieved to fit user's interests. comprehensive annotation of these arrays will benefit chicken researchers, because they will be able to functionally model their expressed dataset to obtain relevant information about their biological system. however, most arrays are not associated to any functional information. the only array that is comprehensively annotated to go is the affymetrix chicken genechip array. this array is the mostly used for gene expression studies as shown in a survey when the chicken research community was polled in july http://doodle.com/participation.html?pollid=zwvmhpt5t23tvfv8). the affymetrix netaffx database links probesets on affymetrix genchip microarrays to go using data from the go consortium. however, the go evidence codes are not linked to any reference that was used to make functional assertions. this is a challenge to researchers who want to associate their dataset with functional information at the same time showing supporting evidence. for example, use of an experimental evidence code in a go annotation should be associated with a paper that displays results from a physical characterization of a gene/gene product being annotated. this allows the researcher to access the detailed information that was used to make the go annotation. in this study we have re-annotated all gene products associated with probesets on affymetrix chicken genome array using go standards. however, the go describes normal gene or gene product function such that information about which genes are associated with significant diseases and disorders and which are known to be drug targets is not captured using the go. this type of information would clearly benefit researchers in modeling diseases. we therefore used ingenuity pathway analysis to identify significant diseases, disorders, drug targets and types of gene represented on affymetrix chicken genome array. furthermore, we demonstrate how other microarrays can be annotated using the annotations from affymetrix chicken array.  initial assessment of structural and functional annotation of chicken array most of chicken arrays currently available are linked to either gene or gene products but very few of the arrays are annotated to any functional information. the affymetrix chicken array was chosen for this study because it represents most of genomic elements annotated on chicken genome. initial assessment of annotation of affymetrix chicken genome array are shown. over 97% of chicken affymetrix probesets are mapped to genes or gene products in total. other probesets represented on this array are for studying different avian viruses. about 51% of the probesets are associated with go annotations made for genes or gene product. different chicken arrays have different gene products represented on them. column & shows whether the printed transcripts are linked to a gene, mrna, est or protein. go in column indicates go functional annotation linked to gene products represented on these arrays and evd indicates evidence code supporting the functional information. the or in columns – indicates presence or absence of the parameter in that specific column. + or - shows that the array is linked or not linked. *evidence that support the go annotation functional annotation and go annotation quality the go annotation of affymetrix chicken probesets does not show any reference supporting the evidence of the annotation as pointed out in methods section. we re-annotated all gene products represented on this array, regardless of their initial annotations, according to go standards. we were able to increase the number of go annotations in all three ontologies; re-annotation increased the total go annotations by 45%, the number of annotated gene products by 10% and the number of probe sets linked to annotated gene products by 13%. moreover, the quality of the original go annotations in all three go ontologies, as determined by gaq score, was improved by the additional annotations. briefly, the gaq score quantitatively assess the level of detail provided by the go annotation and the type of evidence used to make the annotations. the overall mean gaq score of all annotations regardless of biological ontology, increased from to additional functional information was obtained using the ingenuity pathway analysis tool to identify the significant biological functions, diseases and disorders that are represented on affymetrix chicken genome array. the most significant diseases and disorders represented on this array are cancer and genetic disorders, respectively. cell death was identified to be the most significant molecular and cellular function while organismal survival was the most significant process among the physiological system development. different types of genes and known drug targets were also identified. significant biological functions represented on affymetrix chicken genome array. *based on fisher's exact test p-value ≤ tool for array go mapping improved functional annotation of affymetrix chicken array proved to facilitate the annotation of other arrays, such as the arizona gallus gallus k oligo array v. an array go mapper tool developed in this study was able to map entrez genes, ensembl genes and genbank accessions from the arizona array to affymetrix annotations in order to retrieve go annotations. we successfully identified 79% of genes that were common in both arrays, out of which 72% were mapped to go annotations. the total number of go annotations generated for arizona array was. an example of output generated by agom is shown on additional file which includes only the first gene association lines generated for arizona chicken array. the mean gaq score associated with the go annotations retrieved was and was calculated by summing up all gaq scores of all go associations and dividing these by the number of annotated gene products. these results provide an initial assessment of go annotations available for the arizona chicken array and demonstrates how go annotations can be transferred to identical transcriptional elements represented on multiple arrays. discussion the major challenge that faces microarray researchers is interpretation of hundreds of differentially expressed genes into a biologically relevant context. the gene ontology consortium provides a controlled vocabulary to annotate the biological knowledge associated with genes or gene products. in order to make the functional interpretation of microarray dataset less challenging, microarray developers can associate their arrays with functional information. however, most chicken arrays either have no associated go information or do not follow the go annotation standards. in this study we have re-annotated and improved the go annotation of affymetrix chicken genome array to facilitate annotation of other chicken arrays and microarray experimental datasets. further, we developed the array go mapper tool to generate go annotations for chicken arrays with no go information or for microarray experimental datasets and demonstrated its utility by annotating the arizona chicken array which had no associated go information. by implementing agom researchers will not only obtain functional information for their experimental dataset but will also obtain gaq scores associated with each go term retrieved. this will help researchers determine the quality of annotations made to their datasets and also help tracking the improvement made by any additional go when there are any updates. we also provided additional functional information not covered by the go but is associated with the affymetrix chicken genome array. this additional data broadens the ability of array users to model their datasets, for example infectious disease datasets. the additional information obtained on diseases, disorders and known drug targets represented on this array will provide light to future research in drug and therapy development.  improved amount and quality of go annotations of gene products represented on the affymetrix chicken genome array will help researchers to model their genes of interest to high quality functional information by using agom tool. the existing chicken microarray studies can use agom and this demonstrates how this tool can enhance functional annotation in these studies. annotation of microarrays of other species will be included in the future. the top significant diseases and disorders represented on the chicken array correlate well with how the chicken is used as a biomedical model organism to study human diseases and development. the identified gene types and drug targets allows researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. 
modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. we have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on affymetrix chicken genome array. in addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. we have improved the breadth of functional annotations of the gene products associated with probesets on the affymetrix chicken genome array by 45% and the quality of annotation by 14%. to facilitate functional annotation of other arrays and microarray experimental datasets we developed an array go mapper tool to help researchers to quickly retrieve corresponding functional information for their dataset. the disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. this costs researchers amount of time in searching multiple go databases for functional information. researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using agom tool. results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. the affymetrix genchip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to gene ontology.
 modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. the affymetrix genchip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to gene ontology. however the go annotation data presented by affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. in addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. this costs researchers amount of time in searching multiple go databases for functional information.  we have improved the breadth of functional annotations of the gene products associated with probesets on the affymetrix chicken genome array by 45% and the quality of annotation by 14%. we have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on affymetrix chicken genome array. to facilitate functional annotation of other arrays and microarray experimental datasets we developed an array go mapper tool to help researchers to quickly retrieve corresponding functional information for their dataset.  results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using agom tool. the disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. the go annotation data generated will be available for public use via agbase website and will be updated on regular basis. 20- february sixth annual mcbios conference. transformational bioinformatics: delivering value from genomes starkville, ms, usa 