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Table 1 Sample Gene Ontology terms and GO Trimming results

From: GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets

ID GO Accession GO Term p-value Diff. Genes Total Genes
1 GO:0031532 actin cytoskeleton reorganization 0.00338 5 12
2 GO:0009620 response to fungus 3.04E-09 10 12
3 GO:0006037 cell wall chitin metabolic process 3.04E-09 10 12
3 GO:0044036 cell wall macromolecule metabolic process 3.04E-09 10 12
3 GO:0010383 cell wall polysaccharide metabolic process 3.04E-09 10 12
4 GO:0003796 lysozyme activity 3.04E-09 10 12
  GO:0001101 response to acid 3.04E-09 10 12
5 GO:0046578 regulation of Ras protein signal transduction 6.77E-04 6 13
5 GO:0051056 regulation of small GTPase mediated signal transduction 6.77E-04 6 13
6 GO:0008061 chitin binding 1.21E-08 10 13
7 GO:0006032 chitin catabolic process 1.21E-08 10 13
3 GO:0006030 chitin metabolic process 1.21E-08 10 13
8 GO:0004568 chitinase activity 1.21E-08 10 13
9 GO:0003746 translation elongation factor activity 0.00727 5 14
3 GO:0071554 cell wall organization or biogenesis 3.86E-08 10 14
  GO:0008643 carbohydrate transport 0.0226 5 18
10 GO:0005885 Arp2/3 protein complex 0.0226 5 18
9 GO:0006414 translational elongation 0.00485 6 18
11 GO:0045165 cell fate commitment 0.0284 5 19
  GO:0035091 phosphoinositide binding 0.00652 6 19
7 GO:0006026 aminoglycan catabolic process 2.29E-06 10 19
12 GO:0030126 COPI vesicle coat 0.0140 6 22
12 GO:0030663 COPI coated vesicle membrane 0.0140 6 22
7 GO:0000272 polysaccharide catabolic process 1.36E-06 11 22
13 GO:0003007 heart morphogenesis 0.0175 6 23
12 GO:0030660 Golgi-associated vesicle membrane 0.0215 6 24
12 GO:0030137 COPI-coated vesicle 0.0215 6 24
14 GO:0005859 muscle myosin complex 0.0215 6 24
14 GO:0016460 myosin II complex 0.0215 6 24
15 GO:0001725 stress fiber 0.00546 7 24
15 GO:0032432 actin filament bundle 0.00546 7 24
15 GO:0042641 actomyosin 0.00697 7 25
3, 7 GO:0006022 aminoglycan metabolic process 1.04E-05 11 26
16 GO:0030239 myofibril assembly 0.0134 7 28
16 GO:0031032 actomyosin structure organization 0.00441 8 29
17 GO:0016363 nuclear matrix 0.00134 9 30
17 GO:0034399 nuclear periphery 0.00174 9 31
18 GO:0007586 digestion 4.24E-06 13 33
19 GO:0001726 ruffle 0.0146 8 35
20 GO:0005529 sugar binding 6.58E-06 14 39
3, 7 GO:0005976 polysaccharide metabolic process 2.20E-04 12 40
  GO:0005938 cell cortex 0.0407 8 42
16 GO:0010927 cellular component assembly involved in morphogenesis 0.0174 9 43
21 GO:0022627 cytosolic small ribosomal subunit 1.20E-05 15 46
22 GO:0004322 ferroxidase activity 4.18E-07 17 46
22 GO:0016724 oxidoreductase activity, oxidizing metal ions, oxygen as acceptor 4.18E-07 17 46
6 GO:0030247 polysaccharide binding 7.26E-05 14 47
6 GO:0001871 pattern binding 7.26E-05 14 47
22 GO:0016722 oxidoreductase activity, oxidizing metal ions 1.18E-06 17 49
23 GO:0022625 cytosolic large ribosomal subunit 0.0428 9 50
7 GO:0016052 carbohydrate catabolic process 6.10E-05 15 52
4, 8 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds 5.05E-05 16 57
21 GO:0015935 small ribosomal subunit 1.58E-05 17 58
24 GO:0005200 structural constituent of cytoskeleton 0.0210 11 59
23 GO:0015934 large ribosomal subunit 0.0328 11 63
19 GO:0031252 cell leading edge 0.0364 11 64
4, 8 GO:0016798 hydrolase activity, acting on glycosyl bonds 2.74E-04 16 65
6, 20 GO:0030246 carbohydrate binding 1.64E-04 18 75
2 GO:0051707 response to other organism 0.00451 15 76
21, 23 GO:0022626 cytosolic ribosome 9.78E-06 24 98
25 GO:0016791 phosphatase activity 0.0314 17 111
16 GO:0032989 cellular component morphogenesis 0.0160 18 111
25 GO:0016311 dephosphorylation 0.0365 17 113
26 GO:0003735 structural constituent of ribosome 3.52E-06 28 118
21, 23 GO:0033279 ribosomal subunit 5.92E-06 28 121
1, 16 GO:0030036 actin cytoskeleton organization 0.00597 21 124
21, 23 GO:0044445 cytosolic part 3.27E-05 27 125
7 GO:0009057 macromolecule catabolic process 0.0131 21 133
25 GO:0042578 phosphoric ester hydrolase activity 0.0457 20 142
  GO:0006955 immune response 0.0486 20 143
1, 16 GO:0030029 actin filament-based process 0.0189 22 146
27 GO:0005615 extracellular space 0.00507 24 146
21, 23 GO:0005840 ribosome 8.61E-05 29 146
19 GO:0042995 cell projection 0.00775 24 151
10, 14, 15 GO:0015629 actin cytoskeleton 0.0282 24 169
1, 16 GO:0007010 cytoskeleton organization 0.0115 29 198
3, 7 GO:0005975 carbohydrate metabolic process 0.0121 31 216
9 GO:0006412 translation 4.07E-04 38 229
27 GO:0044421 extracellular region part 0.0135 33 235
21, 23 GO:0030529 ribonucleoprotein complex 0.00101 43 281
24, 26 GO:0005198 structural molecule activity 2.31E-05 53 316
21, 23 GO:0005829 cytosol 0.00275 47 330
27 GO:0005576 extracellular region 0.00841 46 341
9 GO:0003723 RNA binding 5.39E-04 53 356
9 GO:0003676 nucleic acid binding 0.00866 73 588
13, 28 GO:0007275 multicellular organismal development 0.0203 89 764
10, 14, 15, 21, 23 GO:0043232 intracellular non-membrane-bounded organelle 0.0186 95 819
10, 14, 15, 21, 23 GO:0043228 non-membrane-bounded organelle 0.0186 95 819
11, 13, 16, 28 GO:0032502 developmental process 0.0307 105 934
18, 28 GO:0032501 multicellular organismal process 0.0273 119 1067
  1. List of experimentally-derived Gene Ontology terms significantly enriched (p-value ≤ 0.05; no MTC) by the differential gene list. Columns show identifiers for hierarchical connections, GO accession numbers, GO term descriptors, enrichment p-values, numbers of genes in differentially regulated gene list annotated with GO term, and total numbers of genes on microarray annotated with GO term. Terms in plain text are retained after GO Trimming with all uniqueness threshold values. Bolded terms are removed with a 0% threshold. Bolded and italicized terms are additionally removed when 40% is used as uniqueness threshold for GO Trimming, and bolded, italicized and underlined terms are additionally removed with a 50% threshold.