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Coexpression cluster:C4804: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!2.79e-14!659;UBERON:0000481!1.72e-13!347;UBERON:0003104!2.87e-12!238;UBERON:0009142!2.87e-12!238;UBERON:0004923!4.77e-12!57;UBERON:0000475!5.36e-12!365;UBERON:0000062!5.37e-12!511;UBERON:0002100!1.23e-11!216;UBERON:0000467!1.41e-11!625;UBERON:0000480!2.34e-11!626;UBERON:0003102!5.08e-10!95;UBERON:0000486!7.77e-10!82;UBERON:0000064!1.02e-09!219;UBERON:0005631!1.51e-09!14;UBERON:0000158!1.51e-09!14;UBERON:0000923!1.54e-09!604;UBERON:0005291!1.54e-09!604;UBERON:0006598!1.54e-09!604;UBERON:0002532!1.54e-09!604;UBERON:0002050!1.76e-09!605;UBERON:0005423!1.76e-09!605;UBERON:0000922!2.84e-09!612;UBERON:0005256!2.97e-09!143;UBERON:0000914!5.43e-09!83;UBERON:0002329!5.43e-09!83;UBERON:0003077!5.43e-09!83;UBERON:0003059!5.43e-09!83;UBERON:0007282!5.43e-09!83;UBERON:0009618!5.43e-09!83;UBERON:0007285!5.43e-09!83;UBERON:0004290!1.29e-08!70;UBERON:0004119!1.41e-08!169;UBERON:0000925!1.41e-08!169;UBERON:0006595!1.41e-08!169;UBERON:0000926!1.71e-08!448;UBERON:0004120!1.71e-08!448;UBERON:0006603!1.71e-08!448;UBERON:0001444!1.92e-08!48;UBERON:0001134!2.88e-07!61;UBERON:0002036!2.88e-07!61;UBERON:0003082!2.88e-07!61;UBERON:0002385!3.43e-07!63;UBERON:0001015!3.43e-07!63;UBERON:0000383!3.43e-07!63;UBERON:0001007!4.76e-07!155;UBERON:0001555!4.76e-07!155;UBERON:0007026!4.76e-07!155;UBERON:0000161!9.76e-07!35
|ontology_enrichment_uberon=UBERON:0000468!2.79e-14!659;UBERON:0000481!1.72e-13!347;UBERON:0003104!2.87e-12!238;UBERON:0009142!2.87e-12!238;UBERON:0004923!4.77e-12!57;UBERON:0000475!5.36e-12!365;UBERON:0000062!5.37e-12!511;UBERON:0002100!1.23e-11!216;UBERON:0000467!1.41e-11!625;UBERON:0000480!2.34e-11!626;UBERON:0003102!5.08e-10!95;UBERON:0000486!7.77e-10!82;UBERON:0000064!1.02e-09!219;UBERON:0005631!1.51e-09!14;UBERON:0000158!1.51e-09!14;UBERON:0000923!1.54e-09!604;UBERON:0005291!1.54e-09!604;UBERON:0006598!1.54e-09!604;UBERON:0002532!1.54e-09!604;UBERON:0002050!1.76e-09!605;UBERON:0005423!1.76e-09!605;UBERON:0000922!2.84e-09!612;UBERON:0005256!2.97e-09!143;UBERON:0000914!5.43e-09!83;UBERON:0002329!5.43e-09!83;UBERON:0003077!5.43e-09!83;UBERON:0003059!5.43e-09!83;UBERON:0007282!5.43e-09!83;UBERON:0009618!5.43e-09!83;UBERON:0007285!5.43e-09!83;UBERON:0004290!1.29e-08!70;UBERON:0004119!1.41e-08!169;UBERON:0000925!1.41e-08!169;UBERON:0006595!1.41e-08!169;UBERON:0000926!1.71e-08!448;UBERON:0004120!1.71e-08!448;UBERON:0006603!1.71e-08!448;UBERON:0001444!1.92e-08!48;UBERON:0001134!2.88e-07!61;UBERON:0002036!2.88e-07!61;UBERON:0003082!2.88e-07!61;UBERON:0002385!3.43e-07!63;UBERON:0001015!3.43e-07!63;UBERON:0000383!3.43e-07!63;UBERON:0001007!4.76e-07!155;UBERON:0001555!4.76e-07!155;UBERON:0007026!4.76e-07!155;UBERON:0000161!9.76e-07!35
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322862347791792!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.012883791263738!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187584672781032!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296430263990033!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00669369403595088!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249783524340474!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00619524273658835
|tfbs_overrepresentation=0.147255,0.0586687,0.039404,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.324808,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.00153794,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0831028,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.241734,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.0422457,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.00862108,0.0109386,0.269326,0.0177901,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.0166632,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.0547453,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.0042906,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.00157828,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.119261,0.0865903,0.0380459,0.130174,0.059488,0.355018,0.782949,0.0821962,0.051522,0.0319444,0.489965,0.335423,0.0790073,0.261553,0.446302,0.0120704,0.00641099,0.0313047,0.330703,0.395854,0.329568,0.042539,0.0724671,0.271958,0.292154,0.405773,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.00257817,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.0565541,0.223503,0.155672,0.603208,0.283727,0.314747,0.0567394,0.291709,0.120054,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.608919,0.18237,0.346458,0.821217,0.747852,0.0419647,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.163222,0.522083,0.248634,0.281576,0.0271848,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.00204647,0.412837,0.102184,0.546839,0.191921,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.0222308,0.00223439,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.319027,0.278044,0.490301,0.108847,0.228096,0.0642385,0.19763,0.15631,0.0106166,0.421464,0.48267,0.420626,0.516462,0.135248,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.127215,0.0348837,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,8.95617e-05,0.0391885,0.284629,0.262537,0.010587,0.226257,0.00202838,0.41707,0.363685,0.464871,0.166672,0.206222,0.171685,0.284166,0.437176,0.269226,0.339277,0.552319,2.49721e-05,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.0769581,0.347298,0.539392,0.34988,0.136757,0.404569,0.6408,0.0793778,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.0223093,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0129363,0.0179103,0.303939,0.279795,0.0140073,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.026047,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.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0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.0109154,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.000364928,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.153605,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.0370461,0.519327,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.0124298,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.0159074,0.0661495,0.000654973,0.0626744,0.191335,0.148574,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.0339656,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.252227,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.418146,0.0785808,0.449036,0.0162067,0.231447,0.544776,0.43956,0.37006,0.10748,0.022688,0.197484,0.396996,0.36145,0.406019,0.381071,0.0119618,0.643768,0.432035,0.722159,0.0140037,0.000645036,0.50058,0.0217093,0.522904,0.00142909,0.336835,0.227104,0.518585,0.0734371,0.38649,0.284625,0.504757,0.55194,0.729153,0.28907,0.164197,0.462688,0.00506733,0.574635,0.478174,0.00846715,0.468444,0.0366482,0.446557,0.243383,0.0186777,0.0889613,0.73485,0.029557,0.161598,0.405056,0.644754,0.0323708,0.0239796,0.37357,0.00500957,0.477353,0.00492096,0.160298,0.0629574,0.20342,0.200493,0.20558,0.300504,0.25656,0.107337,0.349197,0.0131573,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.00465874,0.616388,0.408413,0.516511,0.322213,0.656109,0.33942,0.61031,0.387276,0.0391112,0.221908,0.180745,0.222037,0.416621,0.416292,0.462712,0.734551,0.579431,0.204817,0.000401229,0.138871,0.103502,0.166905,0.19783,0.0833851,0.056391,0.140384,0.175199,0.00818864,0.373557,0.523625,0.408861,0.365487,0.534741,0.0889149,0.0109626,0.236011,0.203486,0.273398,0.0816179,0.4466,0.351067,0.275347,0.637444,0.305885,0.00285094,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.125961,9.18584e-05,0.220231,0.509064,0.196976,0.191517,0.0254647,0.601877,0.307334,0.0246928,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.0858306,0.138622,0.359231,0.339729,0.197805,0.0690807,0.387069,0.332774,0.52832,0.299887,0.0814305,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.0195357,0.163057,0.219428,0.0233135,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.0358457,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.0111711,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.0208458,0.0315594,0.156465,0.13108,0.256963,0.222798,0.172134,0.0166394,0.0969345,0.202137,0.000591588,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.0120432,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.0240944,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.0457063,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.0597546,0.115817,0.218052,0.0271615,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.0607319,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.0404514,0.101021,0.222548,0.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}}
}}

Revision as of 12:04, 5 September 2012


Full id: C4804_Placental_amniotic_Smooth_chorionic_Amniotic_Mesothelial_Fibroblast



Phase1 CAGE Peaks

Hg19::chr9:132515289..132515300,-p3@PTGES
Hg19::chr9:132515302..132515338,-p1@PTGES
Hg19::chr9:132515340..132515357,-p2@PTGES


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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.25e-14180
muscle precursor cell5.55e-0857
myoblast5.55e-0857
multi-potent skeletal muscle stem cell5.55e-0857
muscle cell6.64e-0854
contractile cell3.21e-0759
fibroblast3.91e-0775
Uber Anatomy
Ontology termp-valuen
multi-cellular organism2.79e-14659
multi-tissue structure1.72e-13347
mesenchyme2.87e-12238
entire embryonic mesenchyme2.87e-12238
organ component layer4.77e-1257
organism subdivision5.36e-12365
organ5.37e-12511
trunk1.23e-11216
anatomical system1.41e-11625
anatomical group2.34e-11626
surface structure5.08e-1095
multilaminar epithelium7.77e-1082
organ part1.02e-09219
extraembryonic membrane1.51e-0914
membranous layer1.51e-0914
germ layer1.54e-09604
embryonic tissue1.54e-09604
presumptive structure1.54e-09604
epiblast (generic)1.54e-09604
embryonic structure1.76e-09605
developing anatomical structure1.76e-09605
embryo2.84e-09612
trunk mesenchyme2.97e-09143
somite5.43e-0983
paraxial mesoderm5.43e-0983
presomitic mesoderm5.43e-0983
presumptive segmental plate5.43e-0983
trunk paraxial mesoderm5.43e-0983
presumptive paraxial mesoderm5.43e-0983
dermomyotome1.29e-0870
endoderm-derived structure1.41e-08169
endoderm1.41e-08169
presumptive endoderm1.41e-08169
mesoderm1.71e-08448
mesoderm-derived structure1.71e-08448
presumptive mesoderm1.71e-08448
subdivision of head1.92e-0848
skeletal muscle tissue2.88e-0761
striated muscle tissue2.88e-0761
myotome2.88e-0761
muscle tissue3.43e-0763
musculature3.43e-0763
musculature of body3.43e-0763
digestive system4.76e-07155
digestive tract4.76e-07155
primitive gut4.76e-07155
orifice9.76e-0735


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
EGR1#195834.988179094810140.008056488137383440.0322862347791792
IRF1#365937.63716375356390.002244692747297240.012883791263738
MAX#414936.452555509007120.003721913834265510.0187584672781032
MYC#460935.22228187160940.007020843755740150.0296430263990033
RAD21#5885310.35503389545630.0009004912073565420.00669369403595088
TFAP2A#7020316.5186343730450.0002218033880766340.00249783524340474
TFAP2C#7022310.80922860986020.0007916746575753130.00619524273658835



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.

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