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

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

Protein Class	Size of Class	Overrepresentation Analysis		# Sets per 1000 in Which Significantly Overrepresented
Protein Class	Size of Class	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

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

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