International Journal of Genomics / 2013 / Article / Tab 1

Research Article

GOLink: Finding Cooccurring Terms across Gene Ontology Namespaces

Table 1

(a) Top 10 terms in the GOLink all_list generated using the query term “regulation of gene expression” (GO:0010468) and applying the evidence code filter “!IEA” and database filter “UniProtKB.” (b) Top 10 terms in the GOLink query_list generated using the query term “regulation of gene expression” (GO:0010468) and applying the evidence code filter “!IEA” and database filter “UniProtKB.” (c) Top 10 terms in the GOLink parchild_list generated using the query term “regulation of gene expression” (GO:0010468) and applying the evidence code filter “!IEA” and database filter “UniProtKB.”
(a)

NamespaceGO_IDGO_NameScore (PR)Score ( %)

cellular_componentGO:0005634Nucleus5.1922.32
biological_processGO:0006355Regulation of transcription, DNA-dependent16.5320.96
biological_processGO:0045893Positive regulation of transcription, DNA-dependent16.5320.7
molecular_functionGO:0003700Sequence-specific DNA binding transcription factor activity14.9820.31
biological_processGO:0045944Positive regulation of transcription from RNA polymerase II promoter16.5318.12
biological_processGO:0045892Negative regulation of transcription, DNA-dependent16.5317.17
cellular_componentGO:0005737Cytoplasm3.2912.55
molecular_functionGO:0005515Protein binding3.1412.49
biological_processGO:0000122Negative regulation of transcription from RNA polymerase II promoter16.5312.06
molecular_functionGO:0003677DNA binding10.0010.11

(b)

NamespaceGO_IDGO_NameScore (PR)Score ( %)

biological_processGO:0010468Regulation of gene expression1556.26100
biological_processGO:0060059Embryonic retina morphogenesis in camera-type eye1141.2619.3
biological_processGO:2000744Positive regulation of anterior head development1556.2618.87
biological_processGO:0072049Comma-shaped body morphogenesis1556.2618.87
biological_processGO:0072050S-shaped body morphogenesis1556.2618.87
biological_processGO:0021937Cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation1556.2618.87
biological_processGO:0072077Renal vesicle morphogenesis1556.2618.87
biological_processGO:0021527Spinal cord association neuron differentiation1414.7918.52
biological_processGO:0061205Paramesonephric duct development1296.8918.18
biological_processGO:0001705Ectoderm formation1296.8918.18

(c)

NamespaceGO_IDGO_NameScore (PR)Score ( %)

biological_processGO:0006355Regulation of transcription, DNA-dependent34.6028.54
molecular_functionGO:0003700Sequence-specific DNA binding transcription factor activity27.1122.2
biological_processGO:0045893Positive regulation of transcription, DNA-dependent8.575.78
biological_processGO:0045892Negative regulation of transcription, DNA-dependent9.445.76
biological_processGO:0006446Regulation of translational initiation38.205.47
molecular_functionGO:0003677DNA binding8.625.36
molecular_functionGO:0003743Translation initiation factor activity25.074.72
cellular_componentGO:0005852Eukaryotic translation initiation factor 3 complex33.374.57
biological_processGO:0000122Negative regulation of transcription from RNA polymerase II promoter8.193.98
biological_processGO:0006357Regulation of transcription from RNA polymerase II promoter12.523.94

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