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Table 4 Overrepresentation analysis by PANTHER protein class of differentially expressed proteins and random sets of proteins

From: Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins

Protein Class Size of Class Overrepresentation Analysis # Sets per 1000 in Which Significantly Overrepresented
p-value q-value Using non-DEPs Using all Proteins
cytoskeletal protein 198 0.001 0.033 2 0
storage protein 25 0.011 0.123 0 7
chaperone 183 0.027 0.209 100 107
transmembrane receptor regulatory 65 0.062 0.312 0 1
lyase 151 0.068 0.312 28 33
nucleic acid binding 2332 0.182 0.697 1 7
cell junction protein 140 0.216 0.71 0 0
isomerase 162 0.266 0.766 21 16
cell adhesion molecule 458 0.317 0.81 0 0
extracellular matrix protein 363 0.393 0.825 0 0
transfer/carrier protein 364 0.395 0.825 3 3
protease 586 0.497 0.953 0 0
membrane traffic protein 372 0.677 0.992 1 1
oxidoreductase 593 0.72 0.992 94 61
kinase 699 0.818 0.992 0 0
hydrolase 1482 0.832 0.992 0 0
defense/immunity protein 561 0.87 0.992 0 0
transferase 1198 0.879 0.992 0 0
signaling molecule 1083 0.915 0.992 0 0
transporter 920 0.933 0.992 0 0
enzyme modulator 1353 0.935 0.992 0 0
transcription factor 1451 0.957 0.992 0 0
receptor 1813 0.992 0.992 0 0
  1. The PANTHER overrepresentation analysis was run on the subset of 63 DEPs and on 1000 subsets of 63 proteins (the number of DEPs identified) randomly sampled from the 770 non-differentially expressed proteins and from all 833 proteins identified by mass spectrometry. Overrepresentation was based on comparison to the reference human genome/proteome. DEP differentially expressed protein, PANTHER PANTHER: Protein ANalysis THrough Evolutionary Relationships