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A gene ontology (GO) analysis was done using the DAVID software and database [30], [31].
A gene ontology (GO) analysis was performed using the DAVID software and database [23], [24].
We analyzed the surface proteins of mES cells according to the Uniprot tissue specificity annotations using the DAVID software [30], [31].
To confirm whether or not the two modules in the CCA network have distinct functions, the enriched molecular functions (MFs), biological processes (BPs), and cellular components (CCs) for genes in the two modules were identified using the DAVID software [23] and setting all cancer genes in the two modules as the background population.
Functional classification of differentially expressed proteins was performed using the DAVID software (http://david.abcc.ncifcrf.gov/).abcc.ncifcrf.gov/
We analysed the enrichment of functional annotation using the DAVID software (Huang et al., 2009b).
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We used the DAVID software on the groups of induced and repressed genes (http://david.abcc.ncifcrf.gov/home.jsp) [7] to detect Gene Ontology groups.
We next used the DAVID software [6] to collect ontological terms [7] associated with all the proteins.
We used the DAVID software to perform GO-BP functional enrichment analysis for each of the 7 modules.
Ontology analysis of each co-expressed group of genes was performed using the DAVID ontology software as previously described [29], [30] using the whole genome as the background dataset and an EASE score < 10−3 considered highly enriched ontology groups.
Finally, the enrichment analyses of DEGs were performed by using the DAVID 6.7 software.
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