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Coexpression cluster:C749: Difference between revisions

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|full_id=C749_Wilms_rhabdomyosarcoma_medulloblastoma_fibrous_retinoblastoma_endometrial_schwannoma
|full_id=C749_Wilms_rhabdomyosarcoma_medulloblastoma_fibrous_retinoblastoma_endometrial_schwannoma
|id=C749
|id=C749
|ontology_enrichment_celltype=CL:0002321!4.37e-30!248;CL:0000220!3.71e-29!246;CL:0000055!2.59e-27!180;CL:0000012!4.02e-18!682;CL:0000066!4.40e-18!254;CL:0000548!5.41e-18!679;CL:0000004!5.41e-18!679;CL:0000255!5.41e-18!679;CL:0002371!4.53e-15!591;CL:0000144!1.70e-14!625;CL:0000222!1.32e-13!119;CL:0000183!1.52e-13!59;CL:0000680!3.06e-13!57;CL:0000056!3.06e-13!57;CL:0000355!3.06e-13!57;CL:0000393!5.35e-13!60;CL:0000211!5.35e-13!60;CL:0000187!3.24e-12!54;CL:0000057!6.33e-10!75;CL:0000192!3.99e-09!42;CL:0000514!3.99e-09!42;CL:0000223!1.20e-08!59;CL:0002076!2.23e-08!43;CL:0000003!2.26e-08!722;CL:0000359!9.72e-08!32
|ontology_enrichment_celltype=CL:0002321!2.57e-31!250;CL:0000548!3.02e-21!679;CL:0000255!3.02e-21!679;CL:0000066!2.84e-19!253;CL:0002371!1.93e-17!588;CL:0000055!1.54e-16!106;CL:0000222!9.49e-14!121;CL:0000183!5.28e-13!59;CL:0000680!7.44e-13!58;CL:0000056!7.44e-13!58;CL:0000355!7.44e-13!58;CL:0000393!9.82e-13!61;CL:0000211!9.82e-13!61;CL:0000187!8.80e-12!55;CL:0000003!1.56e-10!722;CL:0000057!9.84e-10!76;CL:0000223!4.09e-09!58;CL:0000192!5.05e-09!43;CL:0000514!5.05e-09!43;CL:0002076!6.78e-09!42;CL:0000359!1.35e-07!32
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005256!2.25e-19!143;UBERON:0000486!1.25e-16!82;UBERON:0000914!4.34e-16!83;UBERON:0002329!4.34e-16!83;UBERON:0003077!4.34e-16!83;UBERON:0003059!4.34e-16!83;UBERON:0007282!4.34e-16!83;UBERON:0009618!4.34e-16!83;UBERON:0007285!4.34e-16!83;UBERON:0000119!7.45e-16!312;UBERON:0002100!8.37e-16!216;UBERON:0000490!1.61e-15!138;UBERON:0000483!6.78e-15!309;UBERON:0000475!1.50e-14!365;UBERON:0003914!4.68e-14!118;UBERON:0000481!6.80e-14!347;UBERON:0003104!8.79e-14!238;UBERON:0009142!8.79e-14!238;UBERON:0004290!1.46e-13!70;UBERON:0002049!1.08e-12!79;UBERON:0007798!1.08e-12!79;UBERON:0000468!2.33e-11!659;UBERON:0001134!3.29e-11!61;UBERON:0002036!3.29e-11!61;UBERON:0003082!3.29e-11!61;UBERON:0002385!1.43e-10!63;UBERON:0001015!1.43e-10!63;UBERON:0000383!1.43e-10!63;UBERON:0000922!7.17e-10!612;UBERON:0003102!1.45e-09!95;UBERON:0001981!3.52e-09!60;UBERON:0007500!3.52e-09!60;UBERON:0004537!3.52e-09!60;UBERON:0006965!3.52e-09!60;UBERON:0001444!5.11e-09!48;UBERON:0000055!7.57e-09!69;UBERON:0000467!8.43e-09!625;UBERON:0000480!1.39e-08!626;UBERON:0001637!1.75e-08!42;UBERON:0003509!1.75e-08!42;UBERON:0004572!1.75e-08!42;UBERON:0002050!2.00e-08!605;UBERON:0005423!2.00e-08!605;UBERON:0000923!2.03e-08!604;UBERON:0005291!2.03e-08!604;UBERON:0006598!2.03e-08!604;UBERON:0002532!2.03e-08!604;UBERON:0004872!2.57e-08!84;UBERON:0005085!4.81e-08!29;UBERON:0000019!7.10e-08!19;UBERON:0000047!7.10e-08!19;UBERON:0004088!7.10e-08!19;UBERON:0003072!7.10e-08!19;UBERON:0003071!7.10e-08!19;UBERON:0004128!7.10e-08!19;UBERON:0000970!2.20e-07!20;UBERON:0004535!4.37e-07!110;UBERON:0001456!5.38e-07!21
|ontology_enrichment_uberon=UBERON:0000475!2.76e-20!264;UBERON:0000490!7.18e-18!148;UBERON:0003104!1.42e-16!160;UBERON:0009142!1.42e-16!160;UBERON:0000486!2.06e-16!83;UBERON:0007503!4.00e-15!78;UBERON:0000119!9.56e-15!309;UBERON:0000483!7.58e-14!306;UBERON:0003914!1.16e-13!117;UBERON:0005256!2.29e-13!122;UBERON:0002329!3.98e-13!71;UBERON:0003059!3.98e-13!71;UBERON:0007282!3.98e-13!71;UBERON:0004290!3.98e-13!71;UBERON:0009618!3.98e-13!71;UBERON:0007524!5.97e-13!73;UBERON:0002100!7.07e-13!199;UBERON:0003077!7.99e-13!72;UBERON:0007285!7.99e-13!72;UBERON:0002049!3.74e-12!78;UBERON:0007798!3.74e-12!78;UBERON:0001134!1.08e-10!62;UBERON:0002036!1.08e-10!62;UBERON:0003082!1.08e-10!62;UBERON:0003102!5.05e-10!99;UBERON:0002385!6.61e-10!64;UBERON:0001015!6.61e-10!64;UBERON:0000383!6.61e-10!64;UBERON:0000481!7.81e-10!342;UBERON:0000468!8.43e-10!656;UBERON:0000033!2.78e-09!56;UBERON:0007500!8.01e-09!59;UBERON:0001981!8.01e-09!59;UBERON:0004537!8.01e-09!59;UBERON:0006965!8.01e-09!59;UBERON:0001444!1.05e-08!49;UBERON:0001637!1.59e-08!42;UBERON:0003509!1.59e-08!42;UBERON:0004572!1.59e-08!42;UBERON:0000055!1.67e-08!68;UBERON:0000467!3.50e-08!624;UBERON:0000477!4.38e-08!373;UBERON:0000480!5.42e-08!625;UBERON:0004872!6.20e-08!83;UBERON:0000153!1.38e-07!62;UBERON:0007811!1.38e-07!62;UBERON:0000922!2.22e-07!592;UBERON:0005085!2.27e-07!31;UBERON:0000019!3.98e-07!20;UBERON:0000047!3.98e-07!20;UBERON:0010312!3.98e-07!20;UBERON:0004088!3.98e-07!20;UBERON:0010230!3.98e-07!20;UBERON:0003072!3.98e-07!20;UBERON:0004128!3.98e-07!20;UBERON:0003071!3.98e-07!20;UBERON:0000970!9.00e-07!21;UBERON:0002104!9.00e-07!21
|tf_chipseq_enrich=BHLHE40#8553;4:16.3170231079918:7.16950673576926e-05:0.0011276748704473!CTCF#10664;10:4.87296033915911:4.65999095504339e-07:2.20418838475442e-05!E2F1#1869;11:4.90738921487932:2.51269297258347e-08:1.75416538344683e-06!HEY1#23462;11:4.04011104310571:2.1344242734918e-07:1.13733233009801e-05!HNF4G#3174;4:10.455790009617:0.000396230217565117:0.00387434581895733!JUND#3727;7:4.45114978119065:0.000236377425785552:0.00257532046438736!NR3C1#2908;11:14.973023331173:1.17432722508375e-13:1.82780269836844e-11!POLR2A#5430;11:2.14745317655807:0.000223198342238743:0.00248487492432279!TAF1#6872;11:3.34304628574529:1.71447392661505e-06:6.47821788790697e-05!TCF7L2#6934;6:5.87464176171128:0.000195714842587612:0.00235432647373964!TFAP2C#7022;10:9.8265714635093:4.61610782404372e-10:4.48884250498419e-08!ZNF263#10127;11:8.22184163701068:8.59817612641675e-11:9.4128397952499e-09!ZZZ3#26009;7:152.353862458785:7.02064328878409e-15:1.22408842143126e-12
|tf_chipseq_enrich=BHLHE40#8553;4:16.3170231079918:7.16950673576926e-05:0.0011276748704473!CTCF#10664;10:4.87296033915911:4.65999095504339e-07:2.20418838475442e-05!E2F1#1869;11:4.90738921487932:2.51269297258347e-08:1.75416538344683e-06!HEY1#23462;11:4.04011104310571:2.1344242734918e-07:1.13733233009801e-05!HNF4G#3174;4:10.455790009617:0.000396230217565117:0.00387434581895733!JUND#3727;7:4.45114978119065:0.000236377425785552:0.00257532046438736!NR3C1#2908;11:14.973023331173:1.17432722508375e-13:1.82780269836844e-11!POLR2A#5430;11:2.14745317655807:0.000223198342238743:0.00248487492432279!TAF1#6872;11:3.34304628574529:1.71447392661505e-06:6.47821788790697e-05!TCF7L2#6934;6:5.87464176171128:0.000195714842587612:0.00235432647373964!TFAP2C#7022;10:9.8265714635093:4.61610782404372e-10:4.48884250498419e-08!ZNF263#10127;11:8.22184163701068:8.59817612641675e-11:9.4128397952499e-09!ZZZ3#26009;7:152.353862458785:7.02064328878409e-15:1.22408842143126e-12
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345,0.294195,0.189864,0.035341,0.49994,0.418217,0.0524994,0.220551,0.582065,0.598904,0.263853,0.250981,0.476472,0.544895,0.187021,0.257444,0.191052,0.144803,0.120932,0.135307,0.292819,0.49569,0.560857,0.167908,0.505898,0.00185424,0.116017,0.792481,0.000361749,0.137272,0.201882,0.86367,0.380631,0.344691,0.347781,0.0265764,0.100939,0.00023503,0.43591,0.135223,0.000404492,0.187413,0.4347,0.657997,0.592319,0.538309,0.402629,0.000127541,0.629279,0.710696,0.251974,0.50054,0.268916,0.522767,0.000912659,0.443444,0.428369,0.488883,0.426313,0.289378,0.156536,0.129502,0.162791,0.0525549,0.068487,0.407148,0.255865,0.345558,0.396241,0.403546,0.0683621,3.31678e-06,0.17731,0.318785,0.171564,0.208652,0.250155,0.302707,0.434718,0.119189,0.246188,0.695697,0.0018064,0.00695058,0.592704,0.00185428,0.372151,0.543363,0.512553,0.000226965,0.195403,0.163718,2.23019e-05,0.205682,0.506771,0.730433,0.237617,0.067764,0.716786,0.124403,0.388692,0.506277,3.79976e-13,0.000336467,0.571685,0.59446,0.343085,0.225589,0.344355,0.169548,0.308886,0.0108947,0.25036,0.157465,0.348305,0.234465,0.609431,0.457137,0.131401,0.40648,0.155356,0.183897,0.359054,0.300739,0.500395,0.334046,0.600989,0.194141,0.256465,0.251557,0.710509,0.454553,0.548455,0.00237659,0.324886,0.000769577,0.501626,0.198407,0.452722,0.211264,0.540994,0.445539,0.0472464,0.462646,0.239328,0.297755,0.203718,0.435273,0.450432,0.313173,0.460799,0.495664,0.545801,1.68306e-06,0.245675,0.654239,0.00900752,0.371665,0.274764,0.434233,0.356138,0.354821,0.531143,0.505578,0.306067,2.34652e-05,0.650129,0.426094,0.319827,0.0251675,0.330545,0.355935,0.0905574,0.490328,0.29423,0.000140387,0.00493892,0.535384,0.267489,1.27653e-06,0.129535,0.745994,2.05372e-05,0.200162,0.0881438,0.000105176,0.594531,0.618426,1.11112e-26,2.12353e-15,0.126073,0.579811,0.40264,0.150341,0.0164278,0.862706,0.815459,0.887595,0.00362896,0.619107,0.0728212,0.626294,0.0292652,0.00499388,0.373009,0.553662,0.553243,0.489388,0.298979,0.524895,0.00012372,0.977283,9.71473e-11,2.29519e-13,0.8371,3.53094e-16,0.921589,0.632302,0.000125283,0.000985073,4.27794e-06,0.611154,0.01987,0.000309404,0.833271,0.707165,0.0473341,0.175367,3.51162e-10,0.713781,0.481939,0.398025,0.712022,0.0980585,0.218123,0.777522,0.000675673,0.66554,0.885729,0.640351,5.47952e-06,0.837695,7.05736e-18,0.00417559,0.476008,2.53797e-05,0.183676,0.0145399,0.00116559,0.246732,0.000764945,0.216922,1.97947e-06,9.19208e-08,0.00990115,2.69396e-05,0.559768,0.569953,0.7303,0.000138523,0.869349,0.792994,0.00236012,0.129307,1.43405e-07,0.000925454,0.309722,0.749482,0.000267675,0.481099,0.61753,0.374787,0.706587,0.00405526,0.013638,0.520009,0.0351893,2.57704e-08,9.74109e-14,0.0140003,0.0193191,2.64114e-06,0.980038,0.000185531,0.0619104,0.834052,0.933541,0.00333313,0.313895,5.67018e-06,0.861382,0.861095,0.897492,2.25423e-07,0.0016686,0.568435,0.890112,0.422014,0.231346,0.488066,0.554368,0.273305,0.752172,0.01165,0.506508,0.773368,0.00832596,0.290105,0.00018161,0.0884557,0.939529,0.274127,0.230874,0.627335,0.56578,0.00132753,0.822354,0.637925,0.00126916,0.692997,0.00163922,0.151906,0.636412,0.093544,0.738902,0.734805,2.50398e-06,0.267149,1.84989e-05,0.653388,0.830046,0.00827787,0.923941,0.598324,1.30577e-15,0.552624,0.541372,0.898217,5.33563e-05,0.389534,0.659228,0.0357261,0.36179,0.0894909,0.845937,0.689775,0.00177354,0.692595,0.831373,0.217794,0.00662392,0.781736,0.0486012,2.08377e-11,0.535628,0.773188,0.0226388,0.729428,0.00475263,0.56962,0.509116,0.257235,0.695354,0.569392,0.118164,0.537498,0.666588,0.534569,0.0312682,0.676428,0.478226,0.540379,0.479343,0.596806,0.574762,0.292558,0.307527,0.486305,0.655454,0.825026,0.0959661,0.573809,0.370131,0.515687,0.0458514,0.599595,0.603486,0.453128,0.744402,0.594113,0.195472,0.531493,0.382823,0.557694,0.114406,0.301747,0.384693,0.51672,0.0702006,0.698203,0.0433491,0.402705,0.575463,0.647625,0.602291,0.225542,0.575661,0.679099,0.355997,0.438647,0.615425,0.477261,0.000463991,0.492207,0.134057,0.22178,0.178456,0.157134,0.109358,0.562004,0.794455,0.000448255,0.374709,0.316768,0.343584,0.201618,0.590141,0.468824,0.598491,0.549025,0.385114,0.66787,0.740651,0.518267,0.472069,0.664008,0.450676,0.0133342,0.384353,0.526219,0.528383,0.240646,0.0989011,0.671331,0.566369,0.586083,0.0553434,0.429354,0.544513,0.650216,0.363633,0.606456,1.53422e-07,0.501724,0.559644,0.424261,0.552902,0.635262,0.464149,0.402607,0.663459,0.603153,0.49975,0.509988,0.311923,0.563078,0.744036,0.7016,0.594401,0.269963,0.00163552,0.338919,0.182919,0.183452,0.451616,0.257575,0.141393,0.183331,0.756752,0.671299,0.581258,0.533448,0.623052,0.537287,0.267192,0.315214,0.215792,0.379171,0.214946,0.333105,0.222472,0.252354,0.396678,0.345496,0.152456,0.224382,0.291235,0.128266,0.412357,0.205066,0.723546,0.710254,0.790463,0.429017,0.00584663,0.661783,0.00155995,0.611867,0.727272,0.657687,0.511893,0.705698,0.675667,0.404324,0.473851,2.96855e-05,0.557233,6.28951e-06,0.628144,0.000738237,0.363221,0.594194,0.605083,0.361802,0.548539,0.540283,0.70279,0.705047,0.284322,0.482941,6.15069e-06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}}
}}

Revision as of 16:39, 19 October 2012


Full id: C749_Wilms_rhabdomyosarcoma_medulloblastoma_fibrous_retinoblastoma_endometrial_schwannoma



Phase1 CAGE Peaks

Hg19::chr12:66218152..66218174,+p10@HMGA2
Hg19::chr12:66218183..66218209,+p4@HMGA2
Hg19::chr12:66218212..66218244,+p5@HMGA2
Hg19::chr12:66218255..66218304,+p3@HMGA2
Hg19::chr12:66218378..66218401,+p6@HMGA2
Hg19::chr12:66218413..66218418,+p17@HMGA2
Hg19::chr12:66218420..66218439,+p12@HMGA2
Hg19::chr12:66218443..66218461,+p8@HMGA2
Hg19::chr12:66218469..66218477,+p16@HMGA2
Hg19::chr12:66218573..66218596,+p7@HMGA2
Hg19::chr12:66218598..66218645,+p2@HMGA2


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
organism subdivision2.76e-20264
unilaminar epithelium7.18e-18148
mesenchyme1.42e-16160
entire embryonic mesenchyme1.42e-16160
multilaminar epithelium2.06e-1683
epithelial vesicle4.00e-1578
cell layer9.56e-15309
epithelium7.58e-14306
epithelial tube1.16e-13117
trunk mesenchyme2.29e-13122
somite3.98e-1371
presomitic mesoderm3.98e-1371
presumptive segmental plate3.98e-1371
dermomyotome3.98e-1371
trunk paraxial mesoderm3.98e-1371
dense mesenchyme tissue5.97e-1373
trunk7.07e-13199
paraxial mesoderm7.99e-1372
presumptive paraxial mesoderm7.99e-1372
vasculature3.74e-1278
vascular system3.74e-1278
skeletal muscle tissue1.08e-1062
striated muscle tissue1.08e-1062
myotome1.08e-1062
surface structure5.05e-1099
muscle tissue6.61e-1064
musculature6.61e-1064
musculature of body6.61e-1064
multi-tissue structure7.81e-10342
multi-cellular organism8.43e-10656
head2.78e-0956
epithelial tube open at both ends8.01e-0959
blood vessel8.01e-0959
blood vasculature8.01e-0959
vascular cord8.01e-0959
subdivision of head1.05e-0849
artery1.59e-0842
arterial blood vessel1.59e-0842
arterial system1.59e-0842
vessel1.67e-0868
anatomical system3.50e-08624
anatomical cluster4.38e-08373
anatomical group5.42e-08625
splanchnic layer of lateral plate mesoderm6.20e-0883
anterior region of body1.38e-0762
craniocervical region1.38e-0762
embryo2.22e-07592
ectodermal placode2.27e-0731
camera-type eye3.98e-0720
simple eye3.98e-0720
immature eye3.98e-0720
ocular region3.98e-0720
eyeball of camera-type eye3.98e-0720
optic cup3.98e-0720
optic vesicle3.98e-0720
eye primordium3.98e-0720
eye9.00e-0721
visual system9.00e-0721


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
BHLHE40#8553416.31702310799187.16950673576926e-050.0011276748704473
CTCF#10664104.872960339159114.65999095504339e-072.20418838475442e-05
E2F1#1869114.907389214879322.51269297258347e-081.75416538344683e-06
HEY1#23462114.040111043105712.1344242734918e-071.13733233009801e-05
HNF4G#3174410.4557900096170.0003962302175651170.00387434581895733
JUND#372774.451149781190650.0002363774257855520.00257532046438736
NR3C1#29081114.9730233311731.17432722508375e-131.82780269836844e-11
POLR2A#5430112.147453176558070.0002231983422387430.00248487492432279
TAF1#6872113.343046285745291.71447392661505e-066.47821788790697e-05
TCF7L2#693465.874641761711280.0001957148425876120.00235432647373964
TFAP2C#7022109.82657146350934.61610782404372e-104.48884250498419e-08
ZNF263#10127118.221841637010688.59817612641675e-119.4128397952499e-09
ZZZ3#260097152.3538624587857.02064328878409e-151.22408842143126e-12



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.