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. Author manuscript; available in PMC: 2014 Dec 10.
Published in final edited form as: J Proteome Res. 2010 Oct 1;9(10):5445–5460. doi: 10.1021/pr100678k

Table 3.

Gene Ontology Term Enrichment for Protein Sets with Increased/Decreased Abundancea

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
a

Over-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.