Coexpression cluster:C3540: Difference between revisions
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{{Coexpression_clusters | 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inner membrane!3.94167936296023e-05!1329;7384;4716$GO:0019866!organelle inner membrane!3.94167936296023e-05!1329;7384;4716$GO:0031966!mitochondrial membrane!4.39079275427809e-05!1329;7384;4716$GO:0005740!mitochondrial envelope!4.39079275427809e-05!1329;7384;4716$GO:0044429!mitochondrial part!7.57771798962151e-05!1329;7384;4716$GO:0031967!organelle envelope!7.57771798962151e-05!1329;7384;4716$GO:0031975!envelope!7.57771798962151e-05!1329;7384;4716$GO:0006118!electron transport!0.000104063478946275!1329;7384;4716$GO:0005746!mitochondrial respiratory chain!0.000141381126508339!7384;4716$GO:0006091!generation of precursor metabolites and energy!0.000180464480492059!1329;7384;4716$GO:0005739!mitochondrion!0.000198827660296956!1329;7384;4716$GO:0044455!mitochondrial membrane part!0.000269873470898099!7384;4716$GO:0006119!oxidative phosphorylation!0.000430686169885607!7384;4716$GO:0031090!organelle membrane!0.00053948090000896!1329;7384;4716$GO:0016491!oxidoreductase activity!0.000549886679035116!1329;7384;4716$GO:0015078!hydrogen ion transmembrane transporter activity!0.000570691170457736!1329;7384$GO:0015077!monovalent inorganic cation transmembrane transporter activity!0.000619459136717262!1329;7384$GO:0022890!inorganic cation transmembrane transporter activity!0.000924073405410639!1329;7384$GO:0044446!intracellular organelle part!0.00772108058328133!1329;7384;4716$GO:0044422!organelle part!0.00772108058328133!1329;7384;4716$GO:0008324!cation transmembrane transporter activity!0.00792935597784679!1329;7384$GO:0016681!oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor!0.00822131044074366!7384$GO:0008121!ubiquinol-cytochrome-c reductase activity!0.00822131044074366!7384$GO:0016679!oxidoreductase activity, acting on diphenols and related substances as donors!0.00822131044074366!7384$GO:0044444!cytoplasmic part!0.00846379679961598!1329;7384;4716$GO:0007585!respiratory gaseous exchange!0.00846379679961598!1329$GO:0045271!respiratory chain complex I!0.0103427143324249!4716$GO:0030964!NADH dehydrogenase complex (quinone)!0.0103427143324249!4716$GO:0005747!mitochondrial respiratory chain complex I!0.0103427143324249!4716$GO:0004129!cytochrome-c oxidase activity!0.0103427143324249!1329$GO:0016675!oxidoreductase activity, acting on heme group of donors!0.0103427143324249!1329$GO:0016676!oxidoreductase activity, acting on heme group of donors, oxygen as acceptor!0.0103427143324249!1329$GO:0015002!heme-copper terminal oxidase activity!0.0103427143324249!1329$GO:0015075!ion transmembrane transporter activity!0.0110499762773029!1329;7384$GO:0009060!aerobic respiration!0.0110499762773029!7384$GO:0006120!mitochondrial electron transport, NADH to ubiquinone!0.0113739705753752!4716$GO:0016310!phosphorylation!0.0114123006757427!7384;4716$GO:0045333!cellular respiration!0.0115721504980818!7384$GO:0022891!substrate-specific transmembrane transporter activity!0.0128118673586426!1329;7384$GO:0008137!NADH dehydrogenase (ubiquinone) activity!0.0128118673586426!4716$GO:0003954!NADH dehydrogenase activity!0.0128118673586426!4716$GO:0050136!NADH dehydrogenase (quinone) activity!0.0128118673586426!4716$GO:0042775!organelle ATP synthesis coupled electron transport!0.0128469912276672!4716$GO:0016655!oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor!0.0128469912276672!4716$GO:0022857!transmembrane transporter activity!0.0128469912276672!1329;7384$GO:0042773!ATP synthesis coupled electron transport!0.0128484456315034!4716$GO:0006793!phosphorus metabolic process!0.0129587858695853!7384;4716$GO:0006796!phosphate metabolic process!0.0129587858695853!7384;4716$GO:0022892!substrate-specific transporter activity!0.013728668980004!1329;7384$GO:0016651!oxidoreductase activity, acting on NADH or NADPH!0.016352482504285!4716$GO:0015980!energy derivation by oxidation of organic compounds!0.017363226964559!7384$GO:0005737!cytoplasm!0.0176623737467382!1329;7384;4716$GO:0004222!metalloendopeptidase activity!0.0274222150223631!7384$GO:0043231!intracellular membrane-bound organelle!0.0274222150223631!1329;7384;4716$GO:0043227!membrane-bound organelle!0.0274222150223631!1329;7384;4716$GO:0009055!electron carrier activity!0.0340569250592044!4716$GO:0016020!membrane!0.0356268822602444!1329;7384;4716$GO:0043229!intracellular organelle!0.0464093602139209!1329;7384;4716$GO:0043226!organelle!0.0464093602139209!1329;7384;4716$GO:0008237!metallopeptidase activity!0.0471924897371985!7384|id=C3540|kegg_enrichment=hsa00190;Oxidative_phosphorylation;8.21E-09!hsa05012;Parkinson's_disease;3.22E-08!hsa05016;Huntington's_disease;7.76E-08!hsa05010;Alzheimer's_disease;1.89E-07!hsa04260;Cardiac_muscle_contraction;1.05E-05!hsa01100;Metabolic_pathways;3.35E-05|ontology_enrichment_celltype=CL:0002321!2.41e-10!250;CL:0000183!4.06e-10!59;CL:0000393!7.42e-09!61;CL:0000211!7.42e-09!61;CL:0000187!2.17e-08!55;CL:0000222!6.02e-08!121;CL:0000680!7.95e-08!58;CL:0000056!7.95e-08!58;CL:0000355!7.95e-08!58;CL:0000192!1.19e-07!43;CL:0000514!1.19e-07!43;CL:0000066!7.06e-07!253;CL:0000055!7.09e-07!106|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000481!1.18e-18!342;UBERON:0007503!2.94e-14!78;UBERON:0003104!5.74e-14!160;UBERON:0009142!5.74e-14!160;UBERON:0000483!1.72e-12!306;UBERON:0000119!3.88e-12!309;UBERON:0000475!4.00e-12!264;UBERON:0007524!7.55e-12!73;UBERON:0003077!7.80e-12!72;UBERON:0007285!7.80e-12!72;UBERON:0005256!9.01e-12!122;UBERON:0002329!1.33e-11!71;UBERON:0003059!1.33e-11!71;UBERON:0007282!1.33e-11!71;UBERON:0004290!1.33e-11!71;UBERON:0009618!1.33e-11!71;UBERON:0002100!1.64e-11!199;UBERON:0000477!3.78e-11!373;UBERON:0000486!1.77e-10!83;UBERON:0002385!1.19e-09!64;UBERON:0001015!1.19e-09!64;UBERON:0000383!1.19e-09!64;UBERON:0001134!1.21e-09!62;UBERON:0002036!1.21e-09!62;UBERON:0003082!1.21e-09!62;UBERON:0000490!1.62e-09!148;UBERON:0000064!3.86e-09!218;UBERON:0003914!4.23e-09!117;UBERON:0000025!2.22e-08!192;UBERON:0003103!6.33e-08!68;UBERON:0000922!1.24e-07!592;UBERON:0004111!3.28e-07!240|pathway_enrichment=9.66492387457841e-08;1.52947420315203e-05;3;132;Oxidative phosphorylation (KEGG):00190!6.31961929821581e-05;0.00444479890641179;3;1138;Metabolic pathways (KEGG):01100!2.15074464693702e-05;0.00170177670188892;2;77;Cardiac muscle contraction (KEGG):04260!1.96661053766193e-07;2.48972894068001e-05;3;167;Alzheimer's disease (KEGG):05010!9.22896270049956e-08;1.52947420315203e-05;3;130;Parkinson's disease (KEGG):05012!2.59185625084851e-07;2.73440834464518e-05;3;183;Huntington's disease (KEGG):05016!5.41556645674944e-08;1.52947420315203e-05;3;109;Electron Transport Chain (Wikipathways):WP111!2.20095901611869e-08;1.39320705720313e-05;3;81;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305!3.42164256458367e-06;0.000309414249054495;2;31;{CYCS,35} (Static Module):NA|tf_chipseq_enrich=CTCFL#140690;2:13.1643162393162:0.00743336703699601:0.0306754156779211!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324694781804275!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321507180643085!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.031998918599741!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461316727954534!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761152113762452!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269213988173359!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460343334816001!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470547164388949!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172679465127204!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276116509777606!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457300202120404!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287494140219617!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054185026445323!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328728570954589|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.0460856,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.113083,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0831028,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.0695582,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.782949,0.635872,0.563047,0.823736,0.489965,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.178727,0.615744,0.271958,0.292154,0.405773,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.280025,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.608919,0.18237,0.706298,0.513427,0.747852,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.217247,0.412837,0.671377,0.546839,0.551561,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.278044,0.807485,0.108847,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.516462,0.582303,0.335105,0.144809,0.145539,0.08628,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.2348,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.36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Latest revision as of 12:28, 17 September 2013
Full id: C3540_skeletal_left_heart_Mesenchymal_diaphragm_Alveolar_tongue
Phase1 CAGE Peaks
| Hg19::chr16:2009500..2009584,+ | p1@NDUFB10 |
| Hg19::chr2:98262497..98262549,+ | p1@COX5B |
| Hg19::chr3:48647059..48647102,- | p1@UQCRC1 |
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 |
|---|---|---|---|---|
| 9.66492387457841e-08 | 1.52947420315203e-05 | 3 | 132 | Oxidative phosphorylation (KEGG):00190 |
| 6.31961929821581e-05 | 0.00444479890641179 | 3 | 1138 | Metabolic pathways (KEGG):01100 |
| 2.15074464693702e-05 | 0.00170177670188892 | 2 | 77 | Cardiac muscle contraction (KEGG):04260 |
| 1.96661053766193e-07 | 2.48972894068001e-05 | 3 | 167 | Alzheimer's disease (KEGG):05010 |
| 9.22896270049956e-08 | 1.52947420315203e-05 | 3 | 130 | Parkinson's disease (KEGG):05012 |
| 2.59185625084851e-07 | 2.73440834464518e-05 | 3 | 183 | Huntington's disease (KEGG):05016 |
| 5.41556645674944e-08 | 1.52947420315203e-05 | 3 | 109 | Electron Transport Chain (Wikipathways):WP111 |
| 2.20095901611869e-08 | 1.39320705720313e-05 | 3 | 81 | Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305 |
| 3.42164256458367e-06 | 0.000309414249054495 | 2 | 31 | {CYCS,35} (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:0005743 | mitochondrial inner membrane | 3.94167936296023e-05 |
| GO:0019866 | organelle inner membrane | 3.94167936296023e-05 |
| GO:0031966 | mitochondrial membrane | 4.39079275427809e-05 |
| GO:0005740 | mitochondrial envelope | 4.39079275427809e-05 |
| GO:0044429 | mitochondrial part | 7.57771798962151e-05 |
| GO:0031967 | organelle envelope | 7.57771798962151e-05 |
| GO:0031975 | envelope | 7.57771798962151e-05 |
| GO:0006118 | electron transport | 0.000104063478946275 |
| GO:0005746 | mitochondrial respiratory chain | 0.000141381126508339 |
| GO:0006091 | generation of precursor metabolites and energy | 0.000180464480492059 |
| GO:0005739 | mitochondrion | 0.000198827660296956 |
| GO:0044455 | mitochondrial membrane part | 0.000269873470898099 |
| GO:0006119 | oxidative phosphorylation | 0.000430686169885607 |
| GO:0031090 | organelle membrane | 0.00053948090000896 |
| GO:0016491 | oxidoreductase activity | 0.000549886679035116 |
| GO:0015078 | hydrogen ion transmembrane transporter activity | 0.000570691170457736 |
| GO:0015077 | monovalent inorganic cation transmembrane transporter activity | 0.000619459136717262 |
| GO:0022890 | inorganic cation transmembrane transporter activity | 0.000924073405410639 |
| GO:0044446 | intracellular organelle part | 0.00772108058328133 |
| GO:0044422 | organelle part | 0.00772108058328133 |
| GO:0008324 | cation transmembrane transporter activity | 0.00792935597784679 |
| GO:0016681 | oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor | 0.00822131044074366 |
| GO:0008121 | ubiquinol-cytochrome-c reductase activity | 0.00822131044074366 |
| GO:0016679 | oxidoreductase activity, acting on diphenols and related substances as donors | 0.00822131044074366 |
| GO:0044444 | cytoplasmic part | 0.00846379679961598 |
| GO:0007585 | respiratory gaseous exchange | 0.00846379679961598 |
| GO:0045271 | respiratory chain complex I | 0.0103427143324249 |
| GO:0030964 | NADH dehydrogenase complex (quinone) | 0.0103427143324249 |
| GO:0005747 | mitochondrial respiratory chain complex I | 0.0103427143324249 |
| GO:0004129 | cytochrome-c oxidase activity | 0.0103427143324249 |
| GO:0016675 | oxidoreductase activity, acting on heme group of donors | 0.0103427143324249 |
| GO:0016676 | oxidoreductase activity, acting on heme group of donors, oxygen as acceptor | 0.0103427143324249 |
| GO:0015002 | heme-copper terminal oxidase activity | 0.0103427143324249 |
| GO:0015075 | ion transmembrane transporter activity | 0.0110499762773029 |
| GO:0009060 | aerobic respiration | 0.0110499762773029 |
| GO:0006120 | mitochondrial electron transport, NADH to ubiquinone | 0.0113739705753752 |
| GO:0016310 | phosphorylation | 0.0114123006757427 |
| GO:0045333 | cellular respiration | 0.0115721504980818 |
| GO:0022891 | substrate-specific transmembrane transporter activity | 0.0128118673586426 |
| GO:0008137 | NADH dehydrogenase (ubiquinone) activity | 0.0128118673586426 |
| GO:0003954 | NADH dehydrogenase activity | 0.0128118673586426 |
| GO:0050136 | NADH dehydrogenase (quinone) activity | 0.0128118673586426 |
| GO:0042775 | organelle ATP synthesis coupled electron transport | 0.0128469912276672 |
| GO:0016655 | oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor | 0.0128469912276672 |
| GO:0022857 | transmembrane transporter activity | 0.0128469912276672 |
| GO:0042773 | ATP synthesis coupled electron transport | 0.0128484456315034 |
| GO:0006793 | phosphorus metabolic process | 0.0129587858695853 |
| GO:0006796 | phosphate metabolic process | 0.0129587858695853 |
| GO:0022892 | substrate-specific transporter activity | 0.013728668980004 |
| GO:0016651 | oxidoreductase activity, acting on NADH or NADPH | 0.016352482504285 |
| GO:0015980 | energy derivation by oxidation of organic compounds | 0.017363226964559 |
| GO:0005737 | cytoplasm | 0.0176623737467382 |
| GO:0004222 | metalloendopeptidase activity | 0.0274222150223631 |
| GO:0043231 | intracellular membrane-bound organelle | 0.0274222150223631 |
| GO:0043227 | membrane-bound organelle | 0.0274222150223631 |
| GO:0009055 | electron carrier activity | 0.0340569250592044 |
| GO:0016020 | membrane | 0.0356268822602444 |
| GO:0043229 | intracellular organelle | 0.0464093602139209 |
| GO:0043226 | organelle | 0.0464093602139209 |
| GO:0008237 | metallopeptidase activity | 0.0471924897371985 |
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><br>
| Ontology term | p-value | n |
|---|---|---|
| embryonic cell | 2.41e-10 | 250 |
| contractile cell | 4.06e-10 | 59 |
| electrically responsive cell | 7.42e-09 | 61 |
| electrically active cell | 7.42e-09 | 61 |
| muscle cell | 2.17e-08 | 55 |
| mesodermal cell | 6.02e-08 | 121 |
| muscle precursor cell | 7.95e-08 | 58 |
| myoblast | 7.95e-08 | 58 |
| multi-potent skeletal muscle stem cell | 7.95e-08 | 58 |
| smooth muscle cell | 1.19e-07 | 43 |
| smooth muscle myoblast | 1.19e-07 | 43 |
| epithelial cell | 7.06e-07 | 253 |
| non-terminally differentiated cell | 7.09e-07 | 106 |
| Ontology term | p-value | n |
|---|---|---|
| multi-tissue structure | 1.18e-18 | 342 |
| epithelial vesicle | 2.94e-14 | 78 |
| mesenchyme | 5.74e-14 | 160 |
| entire embryonic mesenchyme | 5.74e-14 | 160 |
| epithelium | 1.72e-12 | 306 |
| cell layer | 3.88e-12 | 309 |
| organism subdivision | 4.00e-12 | 264 |
| dense mesenchyme tissue | 7.55e-12 | 73 |
| paraxial mesoderm | 7.80e-12 | 72 |
| presumptive paraxial mesoderm | 7.80e-12 | 72 |
| trunk mesenchyme | 9.01e-12 | 122 |
| somite | 1.33e-11 | 71 |
| presomitic mesoderm | 1.33e-11 | 71 |
| presumptive segmental plate | 1.33e-11 | 71 |
| dermomyotome | 1.33e-11 | 71 |
| trunk paraxial mesoderm | 1.33e-11 | 71 |
| trunk | 1.64e-11 | 199 |
| anatomical cluster | 3.78e-11 | 373 |
| multilaminar epithelium | 1.77e-10 | 83 |
| muscle tissue | 1.19e-09 | 64 |
| musculature | 1.19e-09 | 64 |
| musculature of body | 1.19e-09 | 64 |
| skeletal muscle tissue | 1.21e-09 | 62 |
| striated muscle tissue | 1.21e-09 | 62 |
| myotome | 1.21e-09 | 62 |
| unilaminar epithelium | 1.62e-09 | 148 |
| organ part | 3.86e-09 | 218 |
| epithelial tube | 4.23e-09 | 117 |
| tube | 2.22e-08 | 192 |
| compound organ | 6.33e-08 | 68 |
| embryo | 1.24e-07 | 592 |
| anatomical conduit | 3.28e-07 | 240 |
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 | 0.826076 |
| MA0006.1 | 0.639288 |
| MA0007.1 | 0.804807 |
| MA0009.1 | 1.3275 |
| MA0014.1 | 1.80735 |
| 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 | 0.904546 |
| MA0050.1 | 0.81185 |
| MA0051.1 | 0.936307 |
| MA0052.1 | 1.24796 |
| MA0055.1 | 0.190716 |
| MA0056.1 | 0 |
| MA0057.1 | 0.333427 |
| MA0058.1 | 0.716037 |
| MA0059.1 | 0.714521 |
| MA0060.1 | 0.492218 |
| MA0061.1 | 0.456531 |
| 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 | 1.74184 |
| 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 | 0.642957 |
| 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 | 1.12079 |
| MA0140.1 | 0.894983 |
| MA0141.1 | 0.712476 |
| MA0142.1 | 1.12317 |
| MA0143.1 | 1.00455 |
| MA0144.1 | 1.31729 |
| MA0145.1 | 1.37817 |
| MA0146.1 | 1.16674 |
| MA0147.1 | 0.565108 |
| MA0148.1 | 0.854239 |
| MA0149.1 | 0.884158 |
| MA0062.2 | 1.141 |
| MA0035.2 | 0.894194 |
| MA0039.2 | 0.432958 |
| MA0138.2 | 1.04628 |
| MA0002.2 | 0.476938 |
| MA0137.2 | 0.666381 |
| MA0104.2 | 0.491226 |
| MA0047.2 | 0.973066 |
| MA0112.2 | 0.731309 |
| 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 | 1.60572 |
| MA0157.1 | 1.09377 |
| MA0158.1 | 0 |
| MA0159.1 | 0.565904 |
| MA0160.1 | 0.871361 |
| MA0161.1 | 0 |
| MA0162.1 | 2.76014 |
| MA0163.1 | 0.122425 |
| MA0164.1 | 1.01792 |
| MA0080.2 | 0.643061 |
| MA0018.2 | 0.987913 |
| MA0099.2 | 0.902716 |
| MA0079.2 | 0.311277 |
| MA0102.2 | 1.88331 |
| MA0258.1 | 0.519674 |
| MA0259.1 | 0.575594 |
| 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 |
|---|---|---|---|---|
| CTCFL#140690 | 2 | 13.1643162393162 | 0.00743336703699601 | 0.0306754156779211 |
| E2F1#1869 | 3 | 4.90738921487932 | 0.00846098534723939 | 0.0324694781804275 |
| E2F6#1876 | 3 | 5.01715573169739 | 0.0079176980688633 | 0.0321507180643085 |
| EGR1#1958 | 3 | 4.98817909481014 | 0.00805648813738344 | 0.031998918599741 |
| ELF1#1997 | 3 | 4.25809795880754 | 0.0129517987505461 | 0.0461316727954534 |
| ETS1#2113 | 3 | 9.72876092220234 | 0.00108584009258484 | 0.00761152113762452 |
| NFKB1#4790 | 3 | 5.48806342419384 | 0.00604938181565543 | 0.0269213988173359 |
| NR3C1#2908 | 2 | 9.98201555411536 | 0.0127847436554717 | 0.0460343334816001 |
| NRF1#4899 | 3 | 12.2102794477109 | 0.000549217240102001 | 0.00470547164388949 |
| PAX5#5079 | 3 | 6.66956553117783 | 0.00337029099967726 | 0.0172679465127204 |
| SIN3A#25942 | 3 | 5.40888472681514 | 0.00631896197799152 | 0.0276116509777606 |
| SMC3#9126 | 2 | 10.0299552299552 | 0.012665637976747 | 0.0457300202120404 |
| STAT1#6772 | 2 | 13.8043916647995 | 0.00677093170844408 | 0.0287494140219617 |
| TAF7#6879 | 3 | 11.4330694049239 | 0.000669018198194583 | 0.0054185026445323 |
| YY1#7528 | 3 | 4.91117074985386 | 0.00844145534180826 | 0.0328728570954589 |
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.
