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Coexpression cluster:C3304: Difference between revisions

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|full_id=C3304_Fibroblast_Smooth_Pericytes_Cardiac_Mesenchymal_Olfactory_Myoblast
|full_id=C3304_Fibroblast_Smooth_Pericytes_Cardiac_Mesenchymal_Olfactory_Myoblast
|id=C3304
|id=C3304
|ontology_enrichment_celltype=CL:0000055!7.40e-24!180;CL:0000057!4.52e-16!75;CL:0000680!2.39e-10!57;CL:0000056!2.39e-10!57;CL:0000355!2.39e-10!57;CL:0000187!2.21e-09!54;CL:0000183!3.38e-09!59;CL:0000136!3.23e-08!15;CL:0000393!3.79e-08!60;CL:0000211!3.79e-08!60;CL:0000192!1.84e-07!42;CL:0000514!1.84e-07!42;CL:0002620!9.99e-07!23
|ontology_enrichment_celltype=CL:0000057!1.92e-15!76;CL:0000680!7.78e-12!58;CL:0000056!7.78e-12!58;CL:0000355!7.78e-12!58;CL:0000183!2.32e-11!59;CL:0000187!8.19e-11!55;CL:0000393!1.16e-09!61;CL:0000211!1.16e-09!61;CL:0000055!1.53e-09!106;CL:0000192!5.44e-09!43;CL:0000514!5.44e-09!43;CL:0000136!1.52e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!1.08e-19!659;UBERON:0000467!1.43e-14!625;UBERON:0000480!3.12e-14!626;UBERON:0000475!6.28e-13!365;UBERON:0000914!9.32e-13!83;UBERON:0002329!9.32e-13!83;UBERON:0003077!9.32e-13!83;UBERON:0003059!9.32e-13!83;UBERON:0007282!9.32e-13!83;UBERON:0009618!9.32e-13!83;UBERON:0007285!9.32e-13!83;UBERON:0000922!1.19e-12!612;UBERON:0000062!2.92e-12!511;UBERON:0002050!5.21e-12!605;UBERON:0005423!5.21e-12!605;UBERON:0000923!1.18e-11!604;UBERON:0005291!1.18e-11!604;UBERON:0006598!1.18e-11!604;UBERON:0002532!1.18e-11!604;UBERON:0004290!1.79e-11!70;UBERON:0002385!2.32e-11!63;UBERON:0001015!2.32e-11!63;UBERON:0000383!2.32e-11!63;UBERON:0001134!4.06e-11!61;UBERON:0002036!4.06e-11!61;UBERON:0003082!4.06e-11!61;UBERON:0002204!3.02e-10!167;UBERON:0000486!7.10e-10!82;UBERON:0007023!7.79e-10!115;UBERON:0005256!4.91e-09!143;UBERON:0000479!5.32e-09!787;UBERON:0000481!7.84e-09!347;UBERON:0000926!3.71e-07!448;UBERON:0004120!3.71e-07!448;UBERON:0006603!3.71e-07!448
|ontology_enrichment_uberon=UBERON:0000468!3.79e-21!656;UBERON:0000467!4.52e-17!624;UBERON:0000480!1.04e-16!625;UBERON:0002050!1.09e-14!564;UBERON:0000923!1.14e-14!560;UBERON:0010316!1.14e-14!560;UBERON:0005291!1.14e-14!560;UBERON:0006598!1.14e-14!560;UBERON:0010317!1.14e-14!560;UBERON:0002532!1.14e-14!560;UBERON:0007524!2.82e-13!73;UBERON:0003077!7.31e-13!72;UBERON:0007285!7.31e-13!72;UBERON:0002385!8.86e-13!64;UBERON:0001015!8.86e-13!64;UBERON:0000383!8.86e-13!64;UBERON:0000922!1.10e-12!592;UBERON:0002329!1.13e-12!71;UBERON:0003059!1.13e-12!71;UBERON:0007282!1.13e-12!71;UBERON:0004290!1.13e-12!71;UBERON:0009618!1.13e-12!71;UBERON:0000062!1.55e-12!503;UBERON:0001134!1.77e-12!62;UBERON:0002036!1.77e-12!62;UBERON:0003082!1.77e-12!62;UBERON:0005423!2.07e-12!581;UBERON:0002204!4.10e-12!167;UBERON:0000926!3.73e-11!315;UBERON:0004120!3.73e-11!315;UBERON:0006603!3.73e-11!315;UBERON:0000486!4.45e-11!83;UBERON:0000479!7.33e-11!773;UBERON:0005256!1.30e-10!122;UBERON:0000481!3.53e-10!342;UBERON:0003104!4.34e-10!160;UBERON:0009142!4.34e-10!160;UBERON:0007503!1.15e-09!78;UBERON:0007023!2.38e-09!114;UBERON:0010314!1.06e-08!132
|tfbs_overrepresentation=0.147255,0.0586687,1.02437e-07,0.0477154,0.199763,0.0460856,0.0430074,2.07206e-05,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.010441,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.0226057,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.00129531,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.00315066,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.00146949,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.0472875,0.0347684,0.064341,0.209032,6.52476e-06,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0124566,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.0109386,0.269326,0.00117529,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,1.26988e-12,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.0174119,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.000469121,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.0160177,0.107145,0.187297,0.122935,0.0284396,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.0010913,0.0458667,0.104357,0.121154,0.1129,0.0549274,0.000921916,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.00177343,5.00041e-08,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.0219021,0.0695832,3.71971e-07,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.003405,0.119261,0.0865903,0.0380459,0.130174,0.0124596,9.24715e-08,1.05586e-10,0.019623,0.051522,5.90968e-10,1.82637e-07,0.0638737,0.00355277,0.261553,0.118991,0.0806291,0.309233,0.49143,0.330703,0.0914012,0.061507,0.53472,0.0724671,0.271958,0.0475727,0.0159894,0.0921263,0.0582602,0.0643874,0.0187414,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.107929,0.0821552,0.463191,0.000107655,0.528324,0.03861,0.370782,0.101703,0.0297533,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.0340949,0.0026262,0.0447111,0.314747,0.00194826,0.0474194,0.0225637,3.45546e-06,0.416816,0.292835,0.0280875,0.115044,0.0807167,0.056723,0.0154652,0.18237,7.24085e-10,4.6495e-09,0.00296206,0.275351,0.236471,0.185661,0.346319,0.00117453,0.270984,0.0772647,0.0340542,0.000896465,0.00691094,0.248634,0.281576,0.0271848,0.163244,0.0670502,0.0730934,0.184794,4.58399e-05,0.00012837,0.0583074,0.0021959,0.0267008,0.188159,0.551561,0.0225539,0.00208206,0.0550136,0.032738,0.0451077,0.0747529,0.229003,1.67378e-06,0.223844,0.00568155,0.294698,0.34331,0.477304,0.289204,0.327108,3.9207e-07,0.0428373,2.30713e-08,0.428671,0.228096,0.336314,0.19763,0.15631,2.77948e-05,0.104858,0.141711,0.420626,0.516462,0.000203002,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.0460163,0.048108,0.284593,0.343734,0.306556,0.305777,0.601433,0.0340602,0.169823,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.0256829,1.63525e-05,0.206222,0.00713629,0.000779217,0.00288466,0.269226,0.339277,2.13553e-05,0.0439467,0.141758,0.124432,0.168058,0.159617,0.0310416,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.0397695,0.0033863,0.347298,0.182325,0.34988,0.0277379,0.404569,0.0204872,0.0793778,0.0562865,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.0216577,0.00303204,0.191777,0.111931,0.28934,0.0435386,0.0515253,0.126478,0.134852,0.10689,0.00427764,0.0627924,0.00151445,0.0179103,0.00605613,0.0434097,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.00797323,0.129156,0.000107423,0.193675,0.000971782,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,4.24693e-05,0.0876426,0.0046858,0.0112557,0.222432,0.107043,2.20551e-05,0.004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81323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.137332,0.0145999,0.0656973,0.0241929,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.000246135,0.170307,0.201033,0.0488949,0.174921,0.0791124,0.0330727,0.0694567,0.02609,0.0394698,0.0596469,0.00236266,0.122476,0.108872,0.11002,0.0376172,0.0286025,0.0470027,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.0027004,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.0105143,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,3.20516e-11,4.65567e-15,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.00049486,1.60279e-05,0.21727,0.289306,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.00174134,0.0608699,0.175319,0.00583965,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,6.94629e-09,0.000141874,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.060512,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.186638,0.174776,0.0948451,0.0384217,0.249049,0.140533,0.00515192,0.257598,0.103667,0.113069,0.025556,0.16791,0.00423976,3.79153e-05,0.166967,0.0190329,0.0813902,0.184948,0.156261,0.0065917,0.0062542,0.0590944,0.247324,0.178389,0.0257622,0.231073,0.407281,6.78596e-05,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.0177337,0.0785808,0.449036,0.407369,0.231447,0.00131394,0.43956,0.0789454,0.0189483,0.120472,0.197484,0.0919774,0.0107863,0.0966095,0.0841307,0.580441,0.276075,0.11074,5.79979e-05,0.390366,7.0773e-05,0.000757632,0.443185,0.522904,3.32586e-07,3.95207e-08,0.227104,0.518585,0.000486104,0.00161115,0.284625,0.504757,0.04783,9.48418e-06,0.28907,0.164197,0.462688,0.287881,0.0113427,0.478174,0.00846715,0.0263888,0.258219,0.446557,0.243383,6.92931e-08,0.0889613,9.92913e-14,0.000194132,0.161598,2.12518e-06,0.000709044,0.150692,1.39964e-07,0.37357,1.03943e-08,0.00442036,1.07991e-09,0.000558506,2.48085e-05,9.29919e-05,0.200493,0.20558,0.300504,0.25656,0.00254768,0.349197,0.383291,0.156104,0.141318,0.00217346,0.00477789,0.000626916,0.354789,0.163828,0.230581,0.120226,0.0448825,0.562405,0.0556238,0.0175523,0.282286,6.0389e-07,0.0165273,0.408413,0.0374737,0.322213,0.000830547,0.0655189,0.000436901,0.387276,0.00694606,0.802166,0.0433137,0.222037,0.102227,0.416292,0.462712,1.39925e-06,0.0019893,0.204817,0.122646,0.138871,3.08861e-07,0.166905,0.19783,0.0833851,0.056391,0.140384,0.175199,0.332919,0.0805711,0.00701509,0.00209775,0.00124345,0.534741,0.39088,0.0758087,0.236011,0.0222706,0.0413386,0.0816179,0.00319628,0.351067,0.275347,1.13608e-05,0.305885,0.241132,0.000122364,0.30666,0.0516603,6.55179e-07,0.386538,0.00602464,0.250964,0.383276,0.125961,0.00582796,0.220231,9.85308e-06,0.196976,0.191517,0.463751,5.00877e-05,0.307334,0.127092,0.283463,0.000222968,0.135386,0.399569,0.273281,0.0114705,0.275089,0.0858306,0.0283414,0.359231,0.339729,0.197805,6.15084e-08,0.0870376,0.0627969,0.00734059,0.299887,8.64162e-05,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.0200828,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.0335483,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.0262794,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.0377094,0.203781,0.21382,0.207559,0.141867,0.193031,0.0339803,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.0219487,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.00497886,0.00210274,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.0488311,0.0457063,0.347036,0.141729,0.0037817,0.255956,0.200105,0.227491,0.0497481,0.253509,0.177664,0.0446853,0.264413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}}
}}

Revision as of 14:59, 19 October 2012


Full id: C3304_Fibroblast_Smooth_Pericytes_Cardiac_Mesenchymal_Olfactory_Myoblast



Phase1 CAGE Peaks

Hg19::chr12:57522399..57522436,+p3@LRP1
Hg19::chr12:57522439..57522458,+p2@LRP1
Hg19::chr12:57522630..57522663,-p@chr12:57522630..57522663
-


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
multi-cellular organism3.79e-21656
anatomical system4.52e-17624
anatomical group1.04e-16625
embryonic structure1.09e-14564
germ layer1.14e-14560
germ layer / neural crest1.14e-14560
embryonic tissue1.14e-14560
presumptive structure1.14e-14560
germ layer / neural crest derived structure1.14e-14560
epiblast (generic)1.14e-14560
dense mesenchyme tissue2.82e-1373
paraxial mesoderm7.31e-1372
presumptive paraxial mesoderm7.31e-1372
muscle tissue8.86e-1364
musculature8.86e-1364
musculature of body8.86e-1364
embryo1.10e-12592
somite1.13e-1271
presomitic mesoderm1.13e-1271
presumptive segmental plate1.13e-1271
dermomyotome1.13e-1271
trunk paraxial mesoderm1.13e-1271
organ1.55e-12503
skeletal muscle tissue1.77e-1262
striated muscle tissue1.77e-1262
myotome1.77e-1262
developing anatomical structure2.07e-12581
musculoskeletal system4.10e-12167
mesoderm3.73e-11315
mesoderm-derived structure3.73e-11315
presumptive mesoderm3.73e-11315
multilaminar epithelium4.45e-1183
tissue7.33e-11773
trunk mesenchyme1.30e-10122
multi-tissue structure3.53e-10342
mesenchyme4.34e-10160
entire embryonic mesenchyme4.34e-10160
epithelial vesicle1.15e-0978
adult organism2.38e-09114
structure with developmental contribution from neural crest1.06e-08132


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


No analysis results for this cluster

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.