. Author manuscript; available in PMC: 2014 Dec 8.

Published in final edited form as: J Proteome Res. 2014 Sep 3;13(10):4398–4423. doi: 10.1021/pr500638h

Table 2. Enrichment of GO Biological Process Terms.

GO ID	GO Name	240-OxS^a		173-OxS^b		121-OxS^c			Quantified^d

		number genes	p-value^e	number genes	p-value^e	number genes	p-value^e	genes	number genes
GO:0042776	mitochondrial ATP synthesis coupled proton transport	11	< 1.0E-17	10	1.20E-14	10	< 1.0E-17	ATP5A1, ATP5B, ATP5C1, ATP5D, ATP5F1, ATP5H, ATP5I, ATP5J, ATP5L, ATP5O	11
GO:0090382	phagosome maturation	11	3.05E-11	11	9.44E-13	11	7.11E-15	ATP6V0A1, ATP6V0D1, ATP6V1A, ATP6V1B2, ATP6V1C1, ATP6V1D, ATP6V1E1, ATP6V1F, ATP6V1G1, ATP6V1H, TCIRG1	16
GO:0033572	transferrin transport	11	2.71E-10	11	8.72E-12	11	6.83E-14	ATP6V0A1, ATP6V0D1, ATPGV1A, ATP6V1B2, ATP6V1C1, ATP6V1D, ATP6V1E1, ATP6V1F, ATP6V1G1, ATP6V1H, TCIRG1	18
GO:0008286	insulin receptor signaling pathway	13	1.53E-08	12	4.48E-09	11	5.32E-10	ATP6V0A1, ATP6V0D1, ATP6V1A, ATP6V1B2, ATP6V1C1, ATP6V1D, ATP6V1E1, ATP6V1F, ATP6V1G1, ATP6V1H, TCIRG1	32
GO:0055085	transmembrane transport	54	1.95E-10	45	1.56E-10	34	8.40E-10	ABCC4, ATP5A1, ATP5B, ATP5C1, ATP5D, ATP5F1, ATP5H, ATP5I, ATP5J, ATP5L, ATP50, ATP6V0A1, ATP6V0D1, ATP6V1A, ATP6V1B2, ATP6V1C1, ATP6V1D, ATP6V1E1, ATP6V1F, ATP6V1G1, ATP6V1H, CCT8, FTH1, FTL, HK1, HMOX1, HSPA1A, HSPA4, L0NP1, PSMD6, RPS27A, SLC39A7, TCIRG1, THBS1	313
GO:0051084	‘de novo’ posttranslational protein folding	10	4.69E-06	10	2.58E-07	9	6.00E-08	CCT2, CCT3, CCT4, CCT5, CCT6A, CCT7, CCT8, HSPH1, TCP1	30
GO:0022904	respiratory electron transport chain	15	1.38E-04	12	2.93E-04	12	4.21E-06	ATP5A1, ATP5B, ATP5C1, ATP5D, ATP5F1, ATP5H, ATP5I, ATP5J, ATP5L, ATP5O, SDHA, SDHB	78
GO:0043066	negative regulation of apoptotic process	41	1.65E-14	29	6.69E-10	15	1.77E-04	AURKB, CEBPB, HMOX1, HSPA1A, HSPA9, POR, PSMD11, PSMD5, PSMD6, RPS27A, SERPINE1, SET, SQSTM1, THBS1, TIMP1	156
GO:0007264	small GTPase mediated signal transduction	19	2.30E-04	15	5.10E-04	9	1.00E-02	FARP1, HMOX1, IQGAP1, KIF14, RAB2A, RAB5A, RAB5B, RND3, SQSTM1	115
GO:0055114	oxidation-reduction process	28	2.07E-01	22	1.64E-01	20	1.10E-02	ABCC4, ALDH18A1, CYB5B, CYB5R3, ECH1, ETHE1, FTH1, GPD2, HADHA, HCCS, HK1, HMOX1, IQGAP1, POR, PTGS1, PYCR1, RPS27A, SDHA, SDHB, SQRDL	334
GO:0006936	muscle contraction	6	8.04E-02	5	6.18E-02	5	1.11E-02	CALD1, CNN1, MYOF, TPM3, TPM4	51
GO:0007155	cell adhesion	18	9.75E-03	13	2.92E-02	10	1.85E-02	ATP5B, COL1A1, KIF14, LGALS1, MFGE8, RND3, SERPINE1, TGFBI, THBS1, TPM4	145
GO:0006986	response to unfolded protein	8	3.75E-02	7	2.03E-02	5	2.71E-02	ATP6V0D1, HSPA1A, HSPA4, HSPH1, THBS1	62
GO:0000209	protein polyubiquitination	21	2.75E-10	17	4.42E-09	5	3.11E-02	PSMD11, PSMD5, PSMD6, RPS27A, UBR5	64

Full set of 121-OxS nodes plus 119 suggested nodes from STRING.

Set of 121-OxS nodes plus 52 nodes suggested by STRING that were quantified.

Set of 121-OxS nodes.

Total number of quantified proteins annotated to the indicated process.

Hypergeometric p values calculated relative to the background of MS quantified proteins.