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Coexpression cluster:C2574: Difference between revisions

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|full_id=C2574_Mesenchymal_Pericytes_Fibroblast_Adipocyte_Nucleus_Meningeal_stomach
|full_id=C2574_Mesenchymal_Pericytes_Fibroblast_Adipocyte_Nucleus_Meningeal_stomach
|id=C2574
|id=C2574
|ontology_enrichment_celltype=CL:0000055!2.60e-27!180;CL:0000057!7.39e-18!75;CL:0000222!1.31e-15!119;CL:0000183!5.37e-11!59;CL:0000680!5.50e-10!57;CL:0000056!5.50e-10!57;CL:0000355!5.50e-10!57;CL:0000187!2.35e-09!54;CL:0000115!8.70e-09!35;CL:0002620!1.89e-08!23;CL:0002078!3.55e-08!44;CL:0000393!5.31e-08!60;CL:0000211!5.31e-08!60;CL:0000136!1.54e-07!15;CL:0002139!1.81e-07!24
|ontology_enrichment_celltype=CL:0000057!2.43e-18!76;CL:0000222!9.31e-17!121;CL:0000183!2.74e-11!59;CL:0000680!1.77e-10!58;CL:0000056!1.77e-10!58;CL:0000355!1.77e-10!58;CL:0000055!2.82e-10!106;CL:0000187!6.05e-10!55;CL:0000115!3.07e-09!36;CL:0002078!8.64e-09!45;CL:0000393!1.44e-08!61;CL:0000211!1.44e-08!61;CL:0002620!2.33e-08!23;CL:0002139!1.13e-07!24;CL:0000136!2.44e-07!15;CL:0000213!3.40e-07!58;CL:0000215!3.40e-07!58;CL:0000192!5.77e-07!43;CL:0000514!5.77e-07!43
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!5.88e-17!659;UBERON:0005256!1.03e-16!143;UBERON:0002049!2.84e-14!79;UBERON:0007798!2.84e-14!79;UBERON:0000490!3.67e-14!138;UBERON:0003914!4.43e-13!118;UBERON:0002100!1.22e-12!216;UBERON:0000475!1.27e-12!365;UBERON:0000467!1.33e-12!625;UBERON:0000914!1.51e-12!83;UBERON:0002329!1.51e-12!83;UBERON:0003077!1.51e-12!83;UBERON:0003059!1.51e-12!83;UBERON:0007282!1.51e-12!83;UBERON:0009618!1.51e-12!83;UBERON:0007285!1.51e-12!83;UBERON:0004290!2.50e-12!70;UBERON:0000480!2.65e-12!626;UBERON:0001009!3.48e-12!113;UBERON:0004872!3.66e-12!84;UBERON:0004535!1.72e-11!110;UBERON:0002385!2.87e-11!63;UBERON:0001015!2.87e-11!63;UBERON:0000383!2.87e-11!63;UBERON:0000486!4.08e-11!82;UBERON:0000119!5.72e-11!312;UBERON:0001134!6.27e-11!61;UBERON:0002036!6.27e-11!61;UBERON:0003082!6.27e-11!61;UBERON:0000055!1.04e-10!69;UBERON:0000483!4.02e-10!309;UBERON:0000477!1.16e-08!286;UBERON:0001981!2.29e-08!60;UBERON:0007500!2.29e-08!60;UBERON:0004537!2.29e-08!60;UBERON:0006965!2.29e-08!60;UBERON:0000481!3.07e-08!347;UBERON:0000926!8.33e-08!448;UBERON:0004120!8.33e-08!448;UBERON:0006603!8.33e-08!448;UBERON:0002417!1.63e-07!61;UBERON:0000916!1.63e-07!61;UBERON:0004111!2.74e-07!241;UBERON:0000922!5.30e-07!612;UBERON:0003104!8.86e-07!238;UBERON:0009142!8.86e-07!238
|ontology_enrichment_uberon=UBERON:0003104!1.16e-19!160;UBERON:0009142!1.16e-19!160;UBERON:0000468!2.94e-18!656;UBERON:0005256!8.41e-17!122;UBERON:0000490!7.64e-16!148;UBERON:0007503!1.62e-14!78;UBERON:0000467!2.09e-14!624;UBERON:0002049!2.19e-14!78;UBERON:0007798!2.19e-14!78;UBERON:0000480!4.37e-14!625;UBERON:0007524!6.36e-13!73;UBERON:0002329!6.79e-13!71;UBERON:0003059!6.79e-13!71;UBERON:0007282!6.79e-13!71;UBERON:0004290!6.79e-13!71;UBERON:0009618!6.79e-13!71;UBERON:0003914!7.21e-13!117;UBERON:0003077!1.53e-12!72;UBERON:0007285!1.53e-12!72;UBERON:0004872!3.20e-12!83;UBERON:0001009!3.34e-12!112;UBERON:0000926!3.86e-12!315;UBERON:0004120!3.86e-12!315;UBERON:0006603!3.86e-12!315;UBERON:0002385!8.22e-12!64;UBERON:0001015!8.22e-12!64;UBERON:0000383!8.22e-12!64;UBERON:0000486!8.45e-12!83;UBERON:0004535!1.67e-11!109;UBERON:0001134!1.72e-11!62;UBERON:0002036!1.72e-11!62;UBERON:0003082!1.72e-11!62;UBERON:0000119!1.80e-11!309;UBERON:0002100!2.18e-11!199;UBERON:0000055!6.73e-11!68;UBERON:0000475!8.97e-11!264;UBERON:0000477!1.33e-10!373;UBERON:0000483!1.34e-10!306;UBERON:0000481!5.28e-09!342;UBERON:0007500!1.90e-08!59;UBERON:0001981!1.90e-08!59;UBERON:0004537!1.90e-08!59;UBERON:0006965!1.90e-08!59;UBERON:0004111!2.88e-07!240;UBERON:0000922!4.16e-07!592;UBERON:0005423!5.47e-07!581;UBERON:0002417!8.50e-07!60;UBERON:0000916!8.50e-07!60;UBERON:0000923!8.65e-07!560;UBERON:0010316!8.65e-07!560;UBERON:0005291!8.65e-07!560;UBERON:0006598!8.65e-07!560;UBERON:0010317!8.65e-07!560;UBERON:0002532!8.65e-07!560
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817810903946973!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186206370427919!HNF4A#3172;4:23.1322903629537:3.48990320893214e-06:0.000115671850599068!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322471319174445!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244474676300832!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106922342713081!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249126775259601
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817810903946973!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186206370427919!HNF4A#3172;4:23.1322903629537:3.48990320893214e-06:0.000115671850599068!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322471319174445!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244474676300832!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106922342713081!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249126775259601
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78782,0.019419,0.0866228,0.271849,0.00477271,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.12751,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.00120516,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.186295,0.173134,0.101893,0.142875,0.167635,0.171311,3.56798e-05,0.189107,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.0360207,0.00342886,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,3.64817e-06,0.286748,0.367925,0.0471607,0.163865,0.226359,3.26743e-07,0.0339072,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.000482136,0.284016,0.0754883,0.299492,0.100006,0.00120288,0.197817,0.251078,0.279874,0.133127,0.016612,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,6.41174e-06,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.0217469,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.0639386,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.00709584,0.21618,0.243266,0.107021,0.238657,0.20272,0.0896967,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.0103352,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.163504,0.459091,0.54832,0.502211,0.296013,0.282366,0.537932,0.459994,0.0392766,0.548059,0.25423,0.490559,0.45013,0.500698,0.472542,0.00670713,0.747471,0.0410736,0.0943307,0.483077,0.590496,0.603763,0.541914,0.627201,7.37619e-09,0.0217959,0.290703,0.622694,0.00208746,0.478691,0.360199,0.0153629,0.0937029,2.29142e-06,0.365494,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.00865679,0.310552,0.000239931,0.483764,9.68504e-05,0.00104728,0.209437,8.88741e-08,0.748403,0.598945,4.40515e-07,0.464001,1.04219e-05,0.579004,1.00678e-05,0.0387841,0.00419679,0.261575,0.257956,0.264245,0.379063,0.326516,0.0391986,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.116739,0.212239,0.294954,0.156999,0.35974,0.301684,0.39549,0.234254,0.357409,6.45925e-11,0.00995016,0.15578,0.620526,0.404625,0.000684584,0.424691,0.0388817,0.479581,0.259048,0.00041289,0.274432,0.284496,0.512545,0.512178,0.563206,0.00957951,0.321001,0.263302,0.192292,0.180735,0.000899481,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.156131,0.454761,0.639483,0.483658,0.122467,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.0485429,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.557967,0.00277992,0.282281,0.0710918,0.2536,0.246827,0.0103145,7.07534e-07,0.387134,0.00990479,0.358813,0.668972,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.215342,0.447581,0.42505,0.254628,0.000319058,0.479347,0.416962,0.264955,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.0292096,0.249415,0.00479755,0.285648,0.427316,0.0140903,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.0025304,0.290415,0.353147,0.112422,0.170886,0.039537,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.0207461,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.00461365,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,5.25768e-06,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.00571761,0.244395,0.106889,0.128632,0.000107739,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.0119686,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.00786668,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.2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}}
}}

Revision as of 14:10, 19 October 2012


Full id: C2574_Mesenchymal_Pericytes_Fibroblast_Adipocyte_Nucleus_Meningeal_stomach



Phase1 CAGE Peaks

Hg19::chr1:236228379..236228402,-p1@NID1
Hg19::chr1:236228403..236228414,-p3@NID1
Hg19::chr1:236228417..236228446,-p2@NID1
Hg19::chr1:236228490..236228507,-p4@NID1


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><br>


Uber Anatomy
Ontology termp-valuen
mesenchyme1.16e-19160
entire embryonic mesenchyme1.16e-19160
multi-cellular organism2.94e-18656
trunk mesenchyme8.41e-17122
unilaminar epithelium7.64e-16148
epithelial vesicle1.62e-1478
anatomical system2.09e-14624
vasculature2.19e-1478
vascular system2.19e-1478
anatomical group4.37e-14625
dense mesenchyme tissue6.36e-1373
somite6.79e-1371
presomitic mesoderm6.79e-1371
presumptive segmental plate6.79e-1371
dermomyotome6.79e-1371
trunk paraxial mesoderm6.79e-1371
epithelial tube7.21e-13117
paraxial mesoderm1.53e-1272
presumptive paraxial mesoderm1.53e-1272
splanchnic layer of lateral plate mesoderm3.20e-1283
circulatory system3.34e-12112
mesoderm3.86e-12315
mesoderm-derived structure3.86e-12315
presumptive mesoderm3.86e-12315
muscle tissue8.22e-1264
musculature8.22e-1264
musculature of body8.22e-1264
multilaminar epithelium8.45e-1283
cardiovascular system1.67e-11109
skeletal muscle tissue1.72e-1162
striated muscle tissue1.72e-1162
myotome1.72e-1162
cell layer1.80e-11309
trunk2.18e-11199
vessel6.73e-1168
organism subdivision8.97e-11264
anatomical cluster1.33e-10373
epithelium1.34e-10306
multi-tissue structure5.28e-09342
epithelial tube open at both ends1.90e-0859
blood vessel1.90e-0859
blood vasculature1.90e-0859
vascular cord1.90e-0859
anatomical conduit2.88e-07240
embryo4.16e-07592
developing anatomical structure5.47e-07581
abdominal segment of trunk8.50e-0760
abdomen8.50e-0760
germ layer8.65e-07560
germ layer / neural crest8.65e-07560
embryonic tissue8.65e-07560
presumptive structure8.65e-07560
germ layer / neural crest derived structure8.65e-07560
epiblast (generic)8.65e-07560


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
CTCF#1066445.360256373075030.001211145381643620.00817810903946973
HEY1#2346244.040111043105710.00375304636917980.0186206370427919
HNF4A#3172423.13229036295373.48990320893214e-060.000115671850599068
TAF1#687243.343046285745290.008005664898701650.0322471319174445
TBP#690843.706770687096390.005296377814784350.0244474676300832
YY1#752844.911170749853860.00171871838055440.0106922342713081
ZNF263#1012748.221841637010680.0002187871180958320.00249126775259601



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.