Coexpression cluster:C4683: Difference between revisions
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{{Coexpression_clusters | 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acid activation!0.000174999140341419!3376;2617$GO:0043039!tRNA aminoacylation!0.000174999140341419!3376;2617$GO:0006418!tRNA aminoacylation for protein translation!0.000174999140341419!3376;2617$GO:0016875!ligase activity, forming carbon-oxygen bonds!0.000174999140341419!3376;2617$GO:0016876!ligase activity, forming aminoacyl-tRNA and related compounds!0.000174999140341419!3376;2617$GO:0004812!aminoacyl-tRNA ligase activity!0.000174999140341419!3376;2617$GO:0006399!tRNA metabolic process!0.000386485029551408!3376;2617$GO:0005625!soluble fraction!0.000389759114775116!3376;2617$GO:0006520!amino acid metabolic process!0.00142466075754636!3376;2617$GO:0006519!amino acid and derivative metabolic process!0.0017073527239818!3376;2617$GO:0009308!amine metabolic process!0.0017073527239818!3376;2617$GO:0004820!glycine-tRNA ligase activity!0.0017073527239818!2617$GO:0006426!glycyl-tRNA aminoacylation!0.0017073527239818!2617$GO:0016874!ligase activity!0.0017073527239818!3376;2617$GO:0006807!nitrogen compound metabolic process!0.00175001427911881!3376;2617$GO:0004822!isoleucine-tRNA ligase activity!0.0019143533411074!3376$GO:0006428!isoleucyl-tRNA aminoacylation!0.0019143533411074!3376$GO:0019752!carboxylic acid metabolic process!0.0019143533411074!3376;2617$GO:0006082!organic acid metabolic process!0.0019143533411074!3376;2617$GO:0000267!cell fraction!0.00232389136198941!3376;2617$GO:0006412!translation!0.003964147193353!3376;2617$GO:0009059!macromolecule biosynthetic process!0.00624735990464482!3376;2617$GO:0030141!secretory granule!0.00624735990464482!2617$GO:0045055!regulated secretory pathway!0.00857402855122935!2617$GO:0044249!cellular biosynthetic process!0.00858732448264697!3376;2617$GO:0009058!biosynthetic process!0.0132407701752879!3376;2617$GO:0005524!ATP binding!0.0161792710118105!3376;2617$GO:0032559!adenyl ribonucleotide binding!0.0161792710118105!3376;2617$GO:0030554!adenyl nucleotide binding!0.0169818384858086!3376;2617$GO:0032553!ribonucleotide binding!0.0227218286099275!3376;2617$GO:0032555!purine ribonucleotide binding!0.0227218286099275!3376;2617$GO:0017076!purine nucleotide binding!0.0236857190230647!3376;2617$GO:0045045!secretory pathway!0.0281591605431612!2617$GO:0016070!RNA metabolic process!0.0290317417570611!3376;2617$GO:0000166!nucleotide binding!0.0297015403698842!3376;2617$GO:0032940!secretion by cell!0.0319161544909049!2617$GO:0016023!cytoplasmic membrane-bound vesicle!0.035806545811623!2617$GO:0031988!membrane-bound vesicle!0.035806545811623!2617$GO:0046903!secretion!0.0380420856223659!2617$GO:0031410!cytoplasmic vesicle!0.0404963451850661!2617$GO:0031982!vesicle!0.0404963451850661!2617$GO:0010467!gene expression!0.0404963451850661!3376;2617$GO:0044267!cellular protein metabolic process!0.0414628423752696!3376;2617$GO:0044260!cellular macromolecule metabolic process!0.0415722779567392!3376;2617$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0426561100799306!3376;2617$GO:0019538!protein metabolic process!0.0426561100799306!3376;2617|id=C4683|ontology_enrichment_celltype=CL:0000548!5.58e-25!679;CL:0000255!5.58e-25!679;CL:0000057!2.46e-12!76;CL:0000003!1.02e-11!722;CL:0002620!1.30e-08!23;CL:0002371!3.53e-08!588;CL:0000055!3.28e-07!106;CL:0002321!7.08e-07!250|ontology_enrichment_disease=DOID:14566!1.04e-26!239;DOID:162!1.03e-25!235;DOID:0050687!2.09e-15!143;DOID:0050686!2.52e-12!137;DOID:305!2.39e-08!106|ontology_enrichment_uberon=UBERON:0002097!2.31e-07!41;UBERON:0002199!3.98e-07!46;UBERON:0002416!3.98e-07!46|pathway_enrichment=4.79354634032066e-06;0.00151715741671149;2;63;Aminoacyl-tRNA biosynthesis (KEGG):00970!0.000216998173040322;0.045786614511508;2;421;Gene Expression (Reactome):REACT_71!2.5771754517853e-07;0.00016313520609801;2;15;{EPRS,15} (Static 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Latest revision as of 14:17, 17 September 2013
Full id: C4683_Preadipocyte_giant_Smooth_Fibroblast_melanoma_Ewing_mesenchymal
Phase1 CAGE Peaks
| Hg19::chr7:30634439..30634572,+ | p1@GARS |
| Hg19::chr9:95055931..95055951,- | p2@IARS |
| Hg19::chr9:95055956..95056004,- | p1@IARS |
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 4.79354634032066e-06 | 0.00151715741671149 | 2 | 63 | Aminoacyl-tRNA biosynthesis (KEGG):00970 |
| 0.000216998173040322 | 0.045786614511508 | 2 | 421 | Gene Expression (Reactome):REACT_71 |
| 2.5771754517853e-07 | 0.00016313520609801 | 2 | 15 | {EPRS,15} (Static Module):NA |
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0043038 | amino acid activation | 0.000174999140341419 |
| GO:0043039 | tRNA aminoacylation | 0.000174999140341419 |
| GO:0006418 | tRNA aminoacylation for protein translation | 0.000174999140341419 |
| GO:0016875 | ligase activity, forming carbon-oxygen bonds | 0.000174999140341419 |
| GO:0016876 | ligase activity, forming aminoacyl-tRNA and related compounds | 0.000174999140341419 |
| GO:0004812 | aminoacyl-tRNA ligase activity | 0.000174999140341419 |
| GO:0006399 | tRNA metabolic process | 0.000386485029551408 |
| GO:0005625 | soluble fraction | 0.000389759114775116 |
| GO:0006520 | amino acid metabolic process | 0.00142466075754636 |
| GO:0006519 | amino acid and derivative metabolic process | 0.0017073527239818 |
| GO:0009308 | amine metabolic process | 0.0017073527239818 |
| GO:0004820 | glycine-tRNA ligase activity | 0.0017073527239818 |
| GO:0006426 | glycyl-tRNA aminoacylation | 0.0017073527239818 |
| GO:0016874 | ligase activity | 0.0017073527239818 |
| GO:0006807 | nitrogen compound metabolic process | 0.00175001427911881 |
| GO:0004822 | isoleucine-tRNA ligase activity | 0.0019143533411074 |
| GO:0006428 | isoleucyl-tRNA aminoacylation | 0.0019143533411074 |
| GO:0019752 | carboxylic acid metabolic process | 0.0019143533411074 |
| GO:0006082 | organic acid metabolic process | 0.0019143533411074 |
| GO:0000267 | cell fraction | 0.00232389136198941 |
| GO:0006412 | translation | 0.003964147193353 |
| GO:0009059 | macromolecule biosynthetic process | 0.00624735990464482 |
| GO:0030141 | secretory granule | 0.00624735990464482 |
| GO:0045055 | regulated secretory pathway | 0.00857402855122935 |
| GO:0044249 | cellular biosynthetic process | 0.00858732448264697 |
| GO:0009058 | biosynthetic process | 0.0132407701752879 |
| GO:0005524 | ATP binding | 0.0161792710118105 |
| GO:0032559 | adenyl ribonucleotide binding | 0.0161792710118105 |
| GO:0030554 | adenyl nucleotide binding | 0.0169818384858086 |
| GO:0032553 | ribonucleotide binding | 0.0227218286099275 |
| GO:0032555 | purine ribonucleotide binding | 0.0227218286099275 |
| GO:0017076 | purine nucleotide binding | 0.0236857190230647 |
| GO:0045045 | secretory pathway | 0.0281591605431612 |
| GO:0016070 | RNA metabolic process | 0.0290317417570611 |
| GO:0000166 | nucleotide binding | 0.0297015403698842 |
| GO:0032940 | secretion by cell | 0.0319161544909049 |
| GO:0016023 | cytoplasmic membrane-bound vesicle | 0.035806545811623 |
| GO:0031988 | membrane-bound vesicle | 0.035806545811623 |
| GO:0046903 | secretion | 0.0380420856223659 |
| GO:0031410 | cytoplasmic vesicle | 0.0404963451850661 |
| GO:0031982 | vesicle | 0.0404963451850661 |
| GO:0010467 | gene expression | 0.0404963451850661 |
| GO:0044267 | cellular protein metabolic process | 0.0414628423752696 |
| GO:0044260 | cellular macromolecule metabolic process | 0.0415722779567392 |
| GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0426561100799306 |
| GO:0019538 | protein metabolic process | 0.0426561100799306 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| animal cell | 5.58e-25 | 679 |
| eukaryotic cell | 5.58e-25 | 679 |
| fibroblast | 2.46e-12 | 76 |
| native cell | 1.02e-11 | 722 |
| skin fibroblast | 1.30e-08 | 23 |
| somatic cell | 3.53e-08 | 588 |
| non-terminally differentiated cell | 3.28e-07 | 106 |
| embryonic cell | 7.08e-07 | 250 |
| Ontology term | p-value | n |
|---|---|---|
| skin of body | 2.31e-07 | 41 |
| integument | 3.98e-07 | 46 |
| integumental system | 3.98e-07 | 46 |
| Ontology term | p-value | n |
|---|---|---|
| disease of cellular proliferation | 1.04e-26 | 239 |
| cancer | 1.03e-25 | 235 |
| cell type cancer | 2.09e-15 | 143 |
| organ system cancer | 2.52e-12 | 137 |
| carcinoma | 2.39e-08 | 106 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 1.0927 |
| MA0004.1 | 1.93041 |
| MA0006.1 | 2.61424 |
| MA0007.1 | 0.804807 |
| MA0009.1 | 1.3275 |
| MA0014.1 | 0.377374 |
| MA0017.1 | 0.686276 |
| MA0019.1 | 0.990656 |
| MA0024.1 | 1.21731 |
| MA0025.1 | 1.46617 |
| MA0027.1 | 2.95767 |
| MA0028.1 | 1.58389 |
| MA0029.1 | 1.23771 |
| MA0030.1 | 1.22561 |
| MA0031.1 | 1.15713 |
| MA0038.1 | 0.94098 |
| MA0040.1 | 1.24388 |
| MA0041.1 | 0.847069 |
| MA0042.1 | 0.810843 |
| MA0043.1 | 1.32783 |
| MA0046.1 | 1.31611 |
| MA0048.1 | 0.341392 |
| MA0050.1 | 0.81185 |
| MA0051.1 | 0.936307 |
| MA0052.1 | 1.24796 |
| MA0055.1 | 0.557638 |
| MA0056.1 | 0 |
| MA0057.1 | 0.333427 |
| MA0058.1 | 0.716037 |
| MA0059.1 | 0.714521 |
| MA0060.1 | 4.27202 |
| MA0061.1 | 1.15625 |
| MA0063.1 | 0 |
| MA0066.1 | 0.941452 |
| MA0067.1 | 1.65513 |
| MA0068.1 | 0.405474 |
| MA0069.1 | 1.31207 |
| MA0070.1 | 1.30033 |
| MA0071.1 | 0.897953 |
| MA0072.1 | 1.29561 |
| MA0073.1 | 0.0185922 |
| MA0074.1 | 0.935474 |
| MA0076.1 | 0.734647 |
| MA0077.1 | 1.28751 |
| MA0078.1 | 1.04495 |
| MA0081.1 | 0.714712 |
| MA0083.1 | 1.33535 |
| MA0084.1 | 1.84562 |
| MA0087.1 | 1.29304 |
| MA0088.1 | 0.257905 |
| MA0089.1 | 0 |
| MA0090.1 | 0.751469 |
| MA0091.1 | 0.829044 |
| MA0092.1 | 0.785956 |
| MA0093.1 | 2.626 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.956299 |
| MA0101.1 | 0.646932 |
| MA0103.1 | 0.628063 |
| MA0105.1 | 0.31555 |
| MA0106.1 | 0.986396 |
| MA0107.1 | 0.556367 |
| MA0108.2 | 1.15387 |
| MA0109.1 | 0 |
| MA0111.1 | 0.767139 |
| MA0113.1 | 1.00436 |
| MA0114.1 | 0.549955 |
| MA0115.1 | 1.57693 |
| MA0116.1 | 0.560723 |
| MA0117.1 | 1.36676 |
| MA0119.1 | 0.695578 |
| MA0122.1 | 1.39371 |
| MA0124.1 | 1.53432 |
| MA0125.1 | 1.44766 |
| MA0130.1 | 0 |
| MA0131.1 | 1.06461 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.35921 |
| MA0136.1 | 0.948776 |
| MA0139.1 | 0.440097 |
| MA0140.1 | 0.894983 |
| MA0141.1 | 0.712476 |
| MA0142.1 | 1.12317 |
| MA0143.1 | 1.00455 |
| MA0144.1 | 0.531867 |
| MA0145.1 | 0.752137 |
| MA0146.1 | 0.348055 |
| MA0147.1 | 1.38767 |
| MA0148.1 | 0.854239 |
| MA0149.1 | 0.884158 |
| MA0062.2 | 1.141 |
| MA0035.2 | 0.894194 |
| MA0039.2 | 0.0526989 |
| MA0138.2 | 1.04628 |
| MA0002.2 | 0.476938 |
| MA0137.2 | 0.666381 |
| MA0104.2 | 1.2307 |
| MA0047.2 | 0.973066 |
| MA0112.2 | 0.264678 |
| MA0065.2 | 0.277623 |
| MA0150.1 | 0.744617 |
| MA0151.1 | 0 |
| MA0152.1 | 0.902317 |
| MA0153.1 | 1.43021 |
| MA0154.1 | 0.312019 |
| MA0155.1 | 0.256269 |
| MA0156.1 | 0.669101 |
| MA0157.1 | 1.09377 |
| MA0158.1 | 0 |
| MA0159.1 | 0.565904 |
| MA0160.1 | 0.871361 |
| MA0161.1 | 0 |
| MA0162.1 | 0.149099 |
| MA0163.1 | 0.122425 |
| MA0164.1 | 1.01792 |
| MA0080.2 | 0.643061 |
| MA0018.2 | 0.987913 |
| MA0099.2 | 0.902716 |
| MA0079.2 | 0.00160703 |
| MA0102.2 | 1.88331 |
| MA0258.1 | 0.519674 |
| MA0259.1 | 1.40979 |
| MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| ATF3#467 | 3 | 22.4631745260087 | 8.81932387510763e-05 | 0.00130077865582879 |
| BATF#10538 | 3 | 24.3578017923036 | 6.91705216281876e-05 | 0.00110241112594633 |
| BCL3#602 | 2 | 23.0314018691589 | 0.00246467476084291 | 0.0138622525363602 |
| CCNT2#905 | 3 | 6.33620157696263 | 0.00393075003576489 | 0.0191118995803189 |
| CEBPB#1051 | 3 | 7.97114762582482 | 0.00197418705528856 | 0.0115813133666956 |
| CTCFL#140690 | 2 | 13.1643162393162 | 0.00743336703699601 | 0.0306948212864473 |
| E2F1#1869 | 3 | 4.90738921487932 | 0.00846098534723939 | 0.0327680813097614 |
| E2F4#1874 | 3 | 12.6680603152844 | 0.000491798700629898 | 0.0043896217840429 |
| E2F6#1876 | 3 | 5.01715573169739 | 0.0079176980688633 | 0.03242682516819 |
| EGR1#1958 | 3 | 4.98817909481014 | 0.00805648813738344 | 0.0322441680237666 |
| ELF1#1997 | 3 | 4.25809795880754 | 0.0129517987505461 | 0.0464899955220059 |
| ETS1#2113 | 3 | 9.72876092220234 | 0.00108584009258484 | 0.00765157907222642 |
| FOS#2353 | 3 | 8.9979553088944 | 0.00137249927241713 | 0.00901921924822076 |
| FOSL2#2355 | 3 | 16.9302006045617 | 0.000206016205317162 | 0.00244085382497097 |
| GABPB1#2553 | 3 | 7.06768383618217 | 0.00283221282541742 | 0.0154800855805825 |
| GATA1#2623 | 3 | 13.5603081438004 | 0.000400961596378263 | 0.00389435768289309 |
| GTF2B#2959 | 2 | 21.2958866228828 | 0.00287818058991141 | 0.0155901821808909 |
| GTF2F1#2962 | 3 | 12.7396608767577 | 0.000483552504743859 | 0.00435923522166111 |
| HDAC2#3066 | 3 | 13.4156202366263 | 0.000414076139985721 | 0.0039353624519036 |
| HMGN3#9324 | 3 | 8.17854772335059 | 0.00182776694216421 | 0.0109192398851784 |
| IRF1#3659 | 3 | 7.6371637535639 | 0.00224469274729724 | 0.0128717655430174 |
| IRF3#3661 | 2 | 31.3213014743264 | 0.00133951467332011 | 0.0088795666751431 |
| JUN#3725 | 3 | 12.5128291923363 | 0.000510331399272625 | 0.00446423494502334 |
| JUND#3727 | 3 | 6.99466394187103 | 0.00292184504273499 | 0.0157670029150666 |
| MAX#4149 | 3 | 6.45255550900712 | 0.00372191383426551 | 0.0187412833969845 |
| MXI1#4601 | 3 | 9.9615716287593 | 0.00101147054125902 | 0.00723342727051157 |
| MYC#4609 | 3 | 5.2222818716094 | 0.00702084375574015 | 0.0296047279152837 |
| NANOG#79923 | 3 | 29.2447784810127 | 3.99627955670032e-05 | 0.000741195952090615 |
| NFKB1#4790 | 3 | 5.48806342419384 | 0.00604938181565543 | 0.0270818032253949 |
| NFYA#4800 | 2 | 12.2837204665537 | 0.00851601140372443 | 0.0324991308873306 |
| NFYB#4801 | 2 | 11.1731955023576 | 0.0102546713505453 | 0.0381623297170609 |
| PAX5#5079 | 3 | 6.66956553117783 | 0.00337029099967726 | 0.0173659194689079 |
| POU2F2#5452 | 3 | 9.10612405774252 | 0.00132416519268213 | 0.00885651543762593 |
| REST#5978 | 3 | 9.65002871612802 | 0.00111263624711459 | 0.00771239244789279 |
| SIN3A#25942 | 3 | 5.40888472681514 | 0.00631896197799152 | 0.0278246930609434 |
| SMARCB1#6598 | 3 | 18.2527157811574 | 0.00016439776067989 | 0.00204034910607808 |
| SP1#6667 | 3 | 5.6983813781409 | 0.00540396270171217 | 0.0247863179887623 |
| SREBF1#6720 | 2 | 31.3372329603255 | 0.0013381626513618 | 0.0088784936881758 |
| SRF#6722 | 3 | 13.7971782621678 | 0.000380661502580019 | 0.00376440741103632 |
| STAT1#6772 | 3 | 20.7065874971992 | 0.000112599244104667 | 0.00155346795971563 |
| TAF7#6879 | 3 | 11.4330694049239 | 0.000669018198194583 | 0.00545658661470083 |
| TCF7L2#6934 | 3 | 10.7701765631373 | 0.000800318129839838 | 0.00617406006517528 |
| THAP1#55145 | 3 | 31.3691446028513 | 3.23800758564397e-05 | 0.000649086898727583 |
| TRIM28#10155 | 2 | 12.3936833635083 | 0.00836834412943847 | 0.0329431395602874 |
| USF1#7391 | 3 | 6.36149927720796 | 0.0038840405729056 | 0.0191188817171932 |
| USF2#7392 | 3 | 12.9921973850696 | 0.000455897939342781 | 0.00423268956236294 |
| YY1#7528 | 3 | 4.91117074985386 | 0.00844145534180826 | 0.0331223336380175 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
This analysis result is provided for C0 - C305 clusters.
