Journal of Proteome Research Table 1. Enrichment Analysis of Diﬀerentially Expressed Proteinsa ARTICLE a The Webgestalt algorithm27,28 was used to identify enriched sets of proteins in a set of 155 diﬀerentially expressed proteins. The top ﬁve ranked categories (based on adjusted p-value) from each database are listed. Enriched categories with >75% proteins up-regulated in SW480Null were classiﬁed as up in SW480Null (green arrow alone) and enriched classes with >75% down regulated in SW480Null were classiﬁed as down in SW480Null (red arrow alone). All others classiﬁed as a mix of up-regulated and down-regulated proteins. The entire data set of 5002 proteins was used as a reference set in the analysis. Databases are abbreviated as follows; GO, gene ontology (BP, biological process, MF, molecular function, CC, cellular component); KEGG, Kyoto Encyclopedia of Genes and Genomes; WP, Wiki Pathways; PC, Pathway Commons; MsigDB, Molecular Signatures Database (TF, transcription factor, miRNA, microRNA, PPI, protein protein interaction, CP, chromosome position). For a given category the enrichment ratio (ER) is the ratio of observed proteins in the 155 protein set to the number expected based on chance. 1189 dx.doi.org/10.1021/pr2009109 |J. Proteome Res. 2012, 11, 1184–1195