Table 3.

Gene Ontology Term Enrichment for Protein Sets with Increased/Decreased Abundance^a

	up-regulated functions				down-regulated functions
category	GO ID	term	x	Benjamini p-value	GO ID	term	x	Benjamini p-value
GO biological	55114	oxidation reduction	28	2.46 × 10−10	6374	nuclear mRNA splicing, via spliceosome	12	6.68 × 10−6
process	44255	cellular lipid metabolic process	23	1.43 × 10−6	375	RNA splicing, via transesterification reactions	12	6.68 × 10−6
	16096	isoprenoid metabolic process	7	2.21 × 10−6	377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	12	6.68 × 10−6
	42221	response to chemical stimulus	23	2.54 × 10−6	16071	mRNA metabolic process	16	3.76 × 10−5
	44248	cellular catabolic process	23	3.79 × 10−6	6397	mRNA processing	15	3.76 × 10−5
	6695	cholesterol biosynthetic process	6	4.60 × 10−6	6394	RNA processing	19	4.07 × 10−5
	6629	lipid metabolic process	24	5.26 × 10−6	6395	RNA splicing	14	5.24 × 10−5
	6091	generation of precursor metabolites and energy	14	6.93 × 10−6	22607	cellular component assembly	11	6.27 × 10−5
	9056	catabolic process	24	1.35 × 10−5	6334	nucleosome assembly	9	7.56 × 10−5
	16126	sterol biosynthetic process	6	2.27 × 10−5	31497	chromatin assembly	9	1.59 × 10−4
GO molecular	16491	oxidoreductase activity	32	2.27 × 10−12	3723	RNA binding	32	4.08 × 10−11
function	3824	catalytic activity	81	2.39 × 10−9	5515	protein binding	104	9.93 × 10−7
	16616	oxidoreductase activity, acting on the CH–OH group of donors, NAD or NADP as acceptor	10	1.66 × 10−6	8092	cytoskeletal protein binding	18	2.45 × 10−5
	9055	electron carrier activity	14	2.36 × 10−6	3779	actin binding	15	2.45 × 10−5
	9055	oxidoreductase activity, acting on CH–OH group of donors	10	2.72 × 10−6	5488	binding	141	4.40 × 10−4
	50662	coenzyme binding	11	4.07 × 10−6	31072	heat shock protein binding	6	1.52 × 10−3
	16651	oxidoreductase activity, acting on NADH or NADPH	8	7.03 × 10−6	43566	structure-specific DNA binding	7	1.72 × 10−3
	48037	cofactor binding	12	1.59 × 10−5	3697	Mol Funct single-stranded DNA binding	5	1.91 × 10−3
	16408	C-acyltransferase activity	4	9.49 × 10−5	3690	double-stranded DNA binding	5	8.36 × 10−3
	3988	acetyl-CoA C-acyltransferase activity	3	9.49 × 10−5	42805	actinin binding	2	1.84 × 10−2
GO cellular component	44444	cytoplasmic part	87	3.32 × 10−21	30530	heterogeneous nuclear ribonucleoprotein complex	8	1.73 × 10−10
	5737	cytoplasm	107	5.53 × 10−20	44424	intracellular part	126	1.39 × 10−8
	323	lytic vacuole	18	1.55 × 10−12	43228	non-membrane-bounded organelle	46	1.39 × 10−8
	5764	lysosome	18	1.55 × 10−12	43232	intracellular non-membrane-bounded organelle	46	1.39 × 10−8
	5773	vacuole	18	8.35 × 10−12	5622	intracellular	128	7.16 × 10−8
	44429	mitochondrial part	24	3.22 × 10−10	30529	ribonucleoprotein complex	22	5.27 × 10−7
	5739	mitochondrion	30	8.71 × 10−10	44446	intracellular organelle part	64	6.01 × 10−7
	44424	intracellular part	114	1.39 × 10−8	44422	organelle part	64	6.01 × 10−7
	31090	organelle membrane	34	6.42 × 10−7	32991	macromolecular complex	47	1.59 × 10−6
	5622	intracellular	114	7.40 × 10−7	5737	cytoplasm	91	1.70 × 10−6

^aOver-representation of GO annotation terms for the separate sets of up- and down-regulated proteins was computed using the BiNGO plug-in for Cytoscape. Each GO category (GOBP, GOCC, and GOMF) was processed separately. Shown are the top scoring 10 annotations for each category, with corresponding GO ID reference number, number of proteins found to be associated with each term (x), and the Benjamini p-value indicating the significance of the enrichment. All proteins found within each term are listed in Supplementary Table S4.