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Coexpression cluster:C2562: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.72e-21!106;DOID:0050687!1.53e-15!143;DOID:299!1.47e-08!25;DOID:1749!2.01e-08!14
|ontology_enrichment_disease=DOID:305!1.72e-21!106;DOID:0050687!1.53e-15!143;DOID:299!1.47e-08!25;DOID:1749!2.01e-08!14
|ontology_enrichment_uberon=UBERON:0004119!2.95e-20!169;UBERON:0000925!2.95e-20!169;UBERON:0006595!2.95e-20!169;UBERON:0001007!2.07e-14!155;UBERON:0001555!2.07e-14!155;UBERON:0007026!2.07e-14!155;UBERON:0004921!4.24e-13!129;UBERON:0004185!4.24e-13!129;UBERON:0001004!1.15e-12!72;UBERON:0000077!3.56e-12!130;UBERON:0000065!1.37e-11!53;UBERON:0008947!3.43e-10!38;UBERON:0003258!3.43e-10!38;UBERON:0000062!9.65e-10!511;UBERON:0000464!1.15e-08!104;UBERON:0005911!1.36e-08!82;UBERON:0001041!1.41e-08!98;UBERON:0006554!1.67e-08!44;UBERON:0000072!2.46e-08!46;UBERON:0005153!3.30e-08!37;UBERON:0001008!4.42e-08!45;UBERON:0000466!1.78e-07!126;UBERON:0005631!2.93e-07!14;UBERON:0000158!2.93e-07!14;UBERON:0005177!4.57e-07!107;UBERON:0005156!6.98e-07!59;UBERON:0000990!6.98e-07!59
|ontology_enrichment_uberon=UBERON:0004119!2.95e-20!169;UBERON:0000925!2.95e-20!169;UBERON:0006595!2.95e-20!169;UBERON:0001007!2.07e-14!155;UBERON:0001555!2.07e-14!155;UBERON:0007026!2.07e-14!155;UBERON:0004921!4.24e-13!129;UBERON:0004185!4.24e-13!129;UBERON:0001004!1.15e-12!72;UBERON:0000077!3.56e-12!130;UBERON:0000065!1.37e-11!53;UBERON:0008947!3.43e-10!38;UBERON:0003258!3.43e-10!38;UBERON:0000062!9.65e-10!511;UBERON:0000464!1.15e-08!104;UBERON:0005911!1.36e-08!82;UBERON:0001041!1.41e-08!98;UBERON:0006554!1.67e-08!44;UBERON:0000072!2.46e-08!46;UBERON:0005153!3.30e-08!37;UBERON:0001008!4.42e-08!45;UBERON:0000466!1.78e-07!126;UBERON:0005631!2.93e-07!14;UBERON:0000158!2.93e-07!14;UBERON:0005177!4.57e-07!107;UBERON:0005156!6.98e-07!59;UBERON:0000990!6.98e-07!59
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106541521290241!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434487817847948!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.610525395423e-05!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074362011739562!JUNB#3726;4:30.6106326598211:1.13787152942193e-06:4.66032018279597e-05!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391901195083592!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157139068550556!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241746320597381!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.00043817813892143!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123192714552934!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000326653726613121!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114593343073223
|tfbs_overrepresentation=0.191353,0.0774498,0.814139,0.0631091,0.257053,0.363996,0.0569281,0.510252,0.043387,0.0341265,0.181435,0.288577,0.243414,3.75122e-05,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,0.172742,0.107781,0.124486,0.0550418,0.276459,0.268949,0.119094,0.186914,0.122514,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,0.788552,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.145553,0.158244,0.0214762,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.273035,0.103044,0.138225,0.0390464,0.194086,0.142115,0.0999599,0.0720888,0.0667453,0.439574,0.00322261,0.113084,0.216289,0.470097,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.0469922,0.0562614,0.150119,0.368178,0.320801,0.0848546,0.268505,0.713984,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.690341,0.199405,0.121709,0.347653,0.0759036,0.0700593,0.184542,0.0491142,0.280878,0.0541957,0.0883058,0.423154,0.187509,0.34189,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.275495,0.182323,0.112709,0.134107,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.000839662,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,0.202388,0.701894,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.258146,0.186826,0.233377,0.0352845,0.0565357,0.153577,0.0984158,0.29227,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.192028,0.346873,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.2321,0.179282,0.564569,0.0715212,0.105131,0.118265,0.182591,0.234755,0.230552,0.0472274,0.205973,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.241581,0.160458,0.292792,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.00794845,0.346995,0.197158,0.265132,0.230439,0.0606832,0.136664,0.158184,0.147626,0.393313,0.218801,0.21271,0.132273,0.0830988,0.134907,0.0181987,0.462724,0.202467,0.208718,0.0972471,0.165147,0.180711,0.112956,0.0797807,0.0790532,0.00016997,0.476758,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.435782,0.00870304,0.109226,0.151958,0.178155,0.107176,0.146021,0.463127,0.15291,0.206234,0.238926,0.239646,0.128521,0.1286,0.207017,0.14037,0.259646,0.0916845,0.112868,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.106603,0.106727,0.12083,0.154253,0.0993998,0.352707,0.0834863,0.324356,0.545829,0.113754,0.0504034,0.169684,0.327364,0.233666,0.869559,0.73998,0.3024,0.20358,0.888682,0.420045,0.73391,0.332539,0.00863402,0.464128,0.0138826,0.0135348,0.414547,0.489273,0.413223,0.000658513,0.137229,0.34505,0.0785304,0.500422,0.0311814,0.0305759,0.341822,0.241524,0.45167,0.234628,0.0386001,0.143893,0.41477,0.279946,0.524104,0.467825,0.051755,0.0526663,0.000600189,0.076794,0.460819,0.511459,0.0126595,0.322903,0.350886,0.380582,0.583749,0.0150105,0.286293,0.239547,0.00171359,0.359128,0.395864,0.109703,0.0782875,0.547291,0.109035,0.0364944,0.0789041,0.000276442,0.537928,0.464342,0.683088,0.714007,0.235444,0.804772,0.899283,0.279301,0.349116,0.302142,0.239545,0.432689,0.640367,0.343881,0.0442147,0.0151189,0.617741,0.626346,0.316925,0.356561,0.573659,0.211506,0.0883859,0.0962508,0.238465,0.70198,0.853221,0.323783,0.508325,0.187096,0.0907578,0.28972,0.54723,0.280307,0.001754,6.55307e-06,0.0596868,0.0984075,0.293026,0.0142709,0.694744,0.0149898,0.372182,0.109146,0.578951,0.0112154,0.41035,0.784024,0.35234,0.180014,0.525923,0.291917,0.421082,0.25441,0.00163829,0.00579711,0.517933,0.584705,0.517001,0.620475,0.926442,0.419676,0.188259,0.189182,0.477589,0.46699,0.187849,0.560187,0.321282,0.198207,0.00193798,0.178485,0.329745,0.175552,0.129238,0.651295,0.370995,0.074448,0.429696,0.386216,0.385297,0.00167285,0.606408,0.627185,0.360203,0.333725,0.447838,0.289666,0.500627,0.16264,0.122807,0.565545,0.287542,0.265037,0.629795,0.167853,0.53531,0.341771,0.106541,0.290547,0.356381,0.184395,0.55524,0.256884,0.206945,0.0520267,0.462531,0.296994,0.244339,0.117049,0.0786167,0.629381,0.376317,0.00278013,0.276604,0.436806,0.576549,0.00550983,0.158149,0.734628,0.397546,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.286156,0.261868,0.541583,0.540322,0.247151,2.30458e-05,0.365815,0.0576261,0.0847761,0.164977,0.175633,0.139918,0.34669,0.0828344,0.4729,0.0238089,0.383126,0.354433,0.48311,0.0614918,6.33763e-06,0.149782,0.136923,0.118103,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.249506,0.432751,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.102433,0.251882,0.172263,0.243319,0.0637178,0.257309,0.500692,0.166608,0.227224,0.238082,0.219023,0.115115,0.124916,0.0149794,0.28498,0.140114,0.00958602,0.00641248,0.224626,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.621787,5.35985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}}
}}

Revision as of 12:01, 5 September 2012


Full id: C2562_Urothelial_Gingival_Keratinocyte_Mammary_Bronchial_Small_Mallassezderived



Phase1 CAGE Peaks

Hg19::chr1:209826369..209826380,-p@chr1:209826369..209826380
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Hg19::chr1:209826396..209826431,-p@chr1:209826396..209826431
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Hg19::chr1:209826442..209826464,-p@chr1:209826442..209826464
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Hg19::chr1:209826486..209826491,-p@chr1:209826486..209826491
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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


No results for this coexpression

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


No GOStat results

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>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.95e-20169
endoderm2.95e-20169
presumptive endoderm2.95e-20169
digestive system2.07e-14155
digestive tract2.07e-14155
primitive gut2.07e-14155
subdivision of digestive tract4.24e-13129
endodermal part of digestive tract4.24e-13129
respiratory system1.15e-1272
mixed endoderm/mesoderm-derived structure3.56e-12130
respiratory tract1.37e-1153
respiratory primordium3.43e-1038
endoderm of foregut3.43e-1038
organ9.65e-10511
anatomical space1.15e-08104
endo-epithelium1.36e-0882
foregut1.41e-0898
urinary system structure1.67e-0844
segment of respiratory tract2.46e-0846
epithelial bud3.30e-0837
renal system4.42e-0845
immaterial anatomical entity1.78e-07126
extraembryonic membrane2.93e-0714
membranous layer2.93e-0714
trunk region element4.57e-07107
reproductive structure6.98e-0759
reproductive system6.98e-0759
Disease
Ontology termp-valuen
carcinoma1.72e-21106
cell type cancer1.53e-15143
adenocarcinoma1.47e-0825
squamous cell carcinoma2.01e-0814


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)

{{{tfbs_overrepresentation_jaspar}}}



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#promotersEnrichmentp-valueq-value
E2F1#186944.907389214879320.001724022357361790.0106541521290241
EP300#203346.77394172622320.0004748459821442640.00434487817847948
ESR1#2099430.76860329615451.11467714392546e-064.610525395423e-05
JUN#3725412.51282919233634.07770316866756e-050.00074362011739562
JUNB#3726430.61063265982111.13787152942193e-064.66032018279597e-05
JUND#372746.994663941871030.000417684217818580.00391901195083592
REST#597849.650028716128020.0001152825614219170.00157139068550556
SMARCB1#6598418.25271578115749.00423392720929e-060.000241746320597381
SMC3#9126415.04493284493281.95092670935632e-050.00043817813892143
STAT3#6774410.51946499715428.16377768286615e-050.00123192714552934
TFAP2A#7020416.5186343730451.34240829060362e-050.000326653726613121
TFAP2C#7022410.80922860986027.32289634782688e-050.00114593343073223



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.