DAVID tests the null hypothesis that genes are uniformly distributed across pathways and biologic functions.
We used IPA's Canonical Pathways database for all changes detected within a tissue, while we used all Gene Ontology terms, COG ontology, Sp_PIR Keyword [ 71, 72], UP_SEQ_Feature [ 71, 72], Interpro [ 73], PIR_Superfamily [ 74], SMART [ 75, 76], and KEGG [ 30, 77, 78] as databases in DAVID for testing each pattern detected by statistical pattern matching.
The ERA genes were analyzed using the "DAVID" tools which test for over-representation of gene ontologies, pathways and protein domains.
To visualize gene expression changes for contigs of a specific function, we examined the expression levels of four functional groups of contigs, chosen based on their inclusion in significant GO terms in the DAVID functional enrichment test.
Human orthologs of the bovine poly-Q encoding genes were enriched for gene expression (UP_Tissue database) in Epithelium (p = 7.6E-13, after Benjamini correction for multiple testing), Brain (p = 7.1E-4, corrected for multiple testing) and Testis (p = 3.8E-2, corrected for multiple testing) (DAVID database).
To globally correct enrichment P-values to control family-wide false discovery rate (e.g., <= 0.05), DAVID provides multiple testing correction techniques like Bonferroni, Benjamini and FDR, which were taken into account during the analysis.
We used the gene lists of q < 0.1 for DAVID annotation, and tested using the Annotation Chart function in DAVID separately for enrichment of genes with greater abundance in Yorkshire endometrium compared to Meishan endometrium, as well as those with greater abundance in Meishan endometrium compared to Yorkshire endometrium.
Subsequently, we loaded these feature genes into the Database for Annotation, Visualization and Integrated Discovery (DAVID) [31] software to test their enrichment in pathways based on a modified Fisher Exact test.
Two widely used competitive gene set methods for analysis of gene expression studies are gene set enrichment analysis (GSEA) [2], which uses a Kolmogorov Smirnov test, and DAVID [3], which uses a Fisher's exact test.
In DAVID annotation system, Fisher Exact test is adopted to measure the gene-enrichment in annotation terms.
The function of each module was identified by the GO enrichment test of DAVID.
