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Coexpression cluster:C2772: Difference between revisions

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|full_id=C2772_mesenchymal_Fibroblast_Cardiac_Smooth_Chondrocyte_Anulus_tenocyte
|full_id=C2772_mesenchymal_Fibroblast_Cardiac_Smooth_Chondrocyte_Anulus_tenocyte
|id=C2772
|id=C2772
|ontology_enrichment_celltype=CL:0000055!1.24e-16!180;CL:0000057!1.76e-12!75;CL:0000048!7.64e-10!430;CL:0002620!3.23e-09!23;CL:0000723!1.34e-08!436;CL:0000680!1.74e-07!57;CL:0000056!1.74e-07!57;CL:0000355!1.74e-07!57;CL:0000034!3.69e-07!444
|ontology_enrichment_celltype=CL:0000057!1.77e-12!76;CL:0000048!8.42e-11!427;CL:0000723!1.65e-09!433;CL:0002620!4.83e-09!23;CL:0000680!4.91e-08!58;CL:0000056!4.91e-08!58;CL:0000355!4.91e-08!58;CL:0000034!5.02e-08!441;CL:0000187!5.30e-07!55
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!1.40e-12!83;UBERON:0002329!1.40e-12!83;UBERON:0003077!1.40e-12!83;UBERON:0003059!1.40e-12!83;UBERON:0007282!1.40e-12!83;UBERON:0009618!1.40e-12!83;UBERON:0007285!1.40e-12!83;UBERON:0004290!4.16e-10!70;UBERON:0002385!2.83e-09!63;UBERON:0001015!2.83e-09!63;UBERON:0000383!2.83e-09!63;UBERON:0001134!1.03e-08!61;UBERON:0002036!1.03e-08!61;UBERON:0003082!1.03e-08!61;UBERON:0007100!2.50e-08!27;UBERON:0000467!5.12e-08!625;UBERON:0000480!8.71e-08!626;UBERON:0002204!1.20e-07!167;UBERON:0000486!2.92e-07!82;UBERON:0000468!2.94e-07!659;UBERON:0000948!3.06e-07!24;UBERON:0005498!3.06e-07!24;UBERON:0004140!3.06e-07!24;UBERON:0009881!3.06e-07!24;UBERON:0004141!3.06e-07!24;UBERON:0003084!3.06e-07!24;UBERON:0007005!3.06e-07!24;UBERON:0004139!3.06e-07!24;UBERON:0004291!3.06e-07!24;UBERON:0000479!4.41e-07!787
|ontology_enrichment_uberon=UBERON:0007524!7.37e-11!73;UBERON:0003077!1.63e-10!72;UBERON:0007285!1.63e-10!72;UBERON:0002329!1.92e-10!71;UBERON:0003059!1.92e-10!71;UBERON:0007282!1.92e-10!71;UBERON:0004290!1.92e-10!71;UBERON:0009618!1.92e-10!71;UBERON:0002385!7.39e-10!64;UBERON:0001015!7.39e-10!64;UBERON:0000383!7.39e-10!64;UBERON:0002204!2.75e-09!167;UBERON:0001134!2.89e-09!62;UBERON:0002036!2.89e-09!62;UBERON:0003082!2.89e-09!62;UBERON:0000467!7.39e-09!624;UBERON:0000926!1.13e-08!315;UBERON:0004120!1.13e-08!315;UBERON:0006603!1.13e-08!315;UBERON:0000480!1.29e-08!625;UBERON:0000479!2.16e-08!773;UBERON:0007100!2.19e-08!27;UBERON:0007503!3.14e-08!78;UBERON:0000468!1.64e-07!656;UBERON:0000486!1.80e-07!83;UBERON:0000948!3.55e-07!24;UBERON:0005498!3.55e-07!24;UBERON:0004140!3.55e-07!24;UBERON:0009881!3.55e-07!24;UBERON:0004141!3.55e-07!24;UBERON:0003084!3.55e-07!24;UBERON:0007005!3.55e-07!24;UBERON:0004139!3.55e-07!24;UBERON:0004291!3.55e-07!24
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268456773222356!CTBP2#1488;4:62.7170003393281:6.45042639894877e-08:3.96513291747976e-06!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768955380795005!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322994528453798
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268456773222356!CTBP2#1488;4:62.7170003393281:6.45042639894877e-08:3.96513291747976e-06!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768955380795005!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322994528453798
|tfbs_overrepresentation=0.191353,0.0774498,2.93951e-08,0.0631091,0.257053,0.363996,0.0569281,0.510252,0.043387,0.0341265,0.181435,0.288577,0.243414,0.0143109,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,0.172742,0.107781,0.000354565,0.0550418,0.276459,0.000312758,0.119094,0.186914,0.122514,0.00379621,0.149094,0.0239693,0.267529,0.00396344,0.00640354,5.55306e-06,0.0568767,0.157159,2.77872e-06,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.145553,0.158244,8.64008e-05,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.0412226,0.103044,0.0100265,0.0390464,0.194086,0.142115,0.0999599,0.0720888,0.0667453,0.0210971,0.0792005,0.00664966,0.216289,0.0267205,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.0118782,0.368178,0.320801,0.0848546,0.268505,6.78362e-06,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.000256999,0.150351,4.67614e-07,0.199405,0.121709,5.8604e-06,0.00295646,0.350158,0.184542,0.0491142,0.280878,0.0541957,0.0883058,0.423154,0.187509,0.34189,0.0302681,0.0450707,0.020224,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.275495,0.182323,0.112709,0.134107,0.000153866,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,0.202388,6.77489e-09,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.258146,0.186826,0.000168201,0.0352845,0.0565357,0.153577,0.0984158,0.29227,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.192028,5.76857e-06,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.2321,0.017128,0.202544,0.0715212,0.105131,0.00728652,0.182591,0.234755,0.230552,0.0472274,9.81045e-05,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.00616175,0.224443,0.140245,0.241581,0.160458,0.292792,0.0114296,0.0622664,0.102951,0.0795624,0.0891668,0.00055164,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.329956,0.346995,0.197158,0.265132,0.230439,0.0606832,0.136664,0.158184,0.147626,0.0143681,0.218801,0.000112661,0.132273,0.0830988,0.134907,0.184613,0.462724,0.202467,0.208718,0.0972471,0.165147,5.60999e-05,0.112956,0.0797807,0.0790532,0.675167,0.137848,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.00284082,0.00870304,0.109226,0.151958,0.178155,0.107176,0.146021,0.129196,0.15291,0.206234,0.238926,0.239646,0.128521,0.1286,0.00174962,0.14037,0.259646,0.0916845,0.687863,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.106603,0.106727,0.12083,0.000691559,0.0993998,6.48747e-06,0.0834863,3.61026e-06,0.545829,0.113754,0.0504034,0.169684,3.14434e-05,0.495926,0.00122927,0.0122628,0.0260311,6.37266e-11,0.00195226,0.420045,0.0114582,0.332539,0.186966,0.464128,0.389374,0.594055,0.414547,0.0308146,0.000230794,0.000658513,0.364388,0.34505,0.369161,0.500422,0.49089,0.323639,0.00157871,0.241524,0.45167,0.234628,0.520726,0.143893,0.002245,0.279946,0.524104,0.467825,0.563725,0.00309806,0.0806606,0.624969,0.0249003,0.511459,0.586668,0.322903,0.350886,0.380582,0.218919,0.398372,0.286293,0.606558,0.036653,0.359128,0.395864,4.0526e-08,0.368633,0.188516,0.0292801,0.00630994,0.369971,0.0117353,0.181193,0.129952,0.683088,0.0384361,0.235444,0.00150123,0.00014169,0.00287093,0.349116,0.302142,0.239545,0.432689,0.00401934,0.343881,0.000424336,0.606382,0.00048534,0.258511,0.316925,0.356561,0.00185814,0.211506,0.0883859,0.0962508,0.238465,0.0346954,0.128535,0.112487,0.508325,0.187096,0.0225709,0.656755,0.54723,0.280307,0.393583,0.076625,0.0596868,0.0984075,0.293026,2.25475e-06,0.332526,6.22959e-07,0.372182,0.429205,0.578951,0.0769243,0.41035,0.00493387,0.35234,2.29793e-10,0.172079,3.06711e-05,0.421082,0.25441,0.202782,0.00104809,0.0378508,0.584705,0.165503,0.620475,0.0497525,0.0179591,0.188259,0.189182,0.477589,0.0260996,0.546448,0.560187,0.321282,0.198207,0.0616078,0.178485,0.329745,0.175552,0.129238,0.651295,0.370995,0.360161,0.429696,0.386216,0.385297,0.346931,0.606408,7.66545e-05,0.360203,0.333725,0.447838,0.289666,0.500627,0.513045,0.452694,0.565545,2.63869e-05,0.265037,0.0186042,0.00010946,0.179179,0.341771,0.424526,0.000847093,0.356381,0.184395,0.194887,0.0766597,0.206945,0.304719,0.462531,0.296994,0.244339,0.117049,0.0786167,0.0185366,1.27465e-11,0.433821,0.0865866,0.436806,0.576549,0.499072,0.744662,0.000454612,0.397546,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.286156,0.0377469,0.0012638,0.00124449,0.247151,0.146385,0.365815,0.0576261,0.382413,0.164977,0.175633,0.000509942,0.000975864,0.000100995,0.0272905,0.0238089,0.00154686,0.354433,0.142001,0.0614918,0.219485,0.149782,0.136923,0.118103,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.249506,0.432751,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.00230282,0.251882,0.172263,0.0323461,0.0637178,0.257309,0.500692,0.166608,0.227224,0.238082,0.219023,0.115115,0.124916,0.0149794,0.0451304,0.140114,0.348988,0.00641248,0.0273633,0.18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3585,0.271662,0.03989,0.171436,0.00177091,0.0691994,0.000309443,0.198844,0.104946,0.127738,0.0232207,0.161213,0.00737926,0.0737069,1.21324e-09,7.00333e-05,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.00283228,0.281453,0.0522771,0.0787278,0.515487,0.013521,0.142462,0.143935,0.00814638,0.0379537,0.000120758,0.0188872,0.051459,0.00686557,0.0726892,0.18732,0.32305,0.278397,0.245002,0.0155048,0.487259,0.00598877,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.000162768,0.36316,0.0625685,0.124464,1.86043e-05,0.0159364,0.101893,0.142875,0.167635,0.171311,9.67642e-08,1.69874e-07,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,4.48492e-07,0.00342886,0.278645,0.0769795,0.155708,0.248017,0.00244747,0.652972,0.0760151,0.00202402,0.143933,0.0803251,0.226641,0.0832234,0.00455803,0.286748,0.367925,0.0471607,0.163865,0.226359,0.000536417,0.00459675,0.265324,0.00461571,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.0448074,0.0754883,0.0501465,0.100006,0.0756617,0.197817,0.251078,0.0434358,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.0153391,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.00720587,0.364334,0.15547,0.000243487,2.10364e-05,0.14794,0.147307,0.240761,0.0277041,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.114979,0.21618,0.243266,0.107021,0.238657,4.1197e-06,0.0896967,0.000471212,0.0780061,0.0559668,0.230477,0.000372597,0.295555,5.75145e-08,0.140541,0.0478217,0.507599,0.170854,0.0575231,0.0161134,0.00640224,0.459091,0.54832,0.00568499,0.296013,0.649813,0.181196,0.127256,0.523209,0.189126,0.25423,0.490559,0.45013,7.26146e-07,0.472542,3.66192e-06,0.747471,1.42941e-05,0.00816509,0.483077,0.590496,0.0147688,1.77808e-05,0.627201,0.00784768,0.142078,0.290703,0.0757071,8.21916e-06,0.478691,0.360199,0.241059,0.0236144,0.0021436,0.365494,0.212703,0.0515679,0.364079,0.680099,0.579886,2.32208e-05,0.206595,0.328518,0.545608,0.310552,1.38473e-06,0.0295909,0.00961647,0.453065,0.209437,6.30105e-07,0.161672,0.232518,0.000386547,0.12974,1.75388e-06,0.0118057,0.00125006,0.0112416,0.000213717,0.261575,0.257956,0.0384726,0.00147206,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.000825542,0.126097,0.3955,0.00305636,0.212239,0.048546,0.156999,0.35974,0.667777,0.014642,0.234254,0.357409,0.00116299,0.000364106,0.50338,0.620526,0.404625,3.31935e-07,0.106633,0.715362,0.479581,0.62689,1.67972e-05,0.0207342,0.044968,0.512545,0.512178,0.201413,0.103692,0.684899,0.263302,0.047857,0.180735,0.0646927,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.0342559,0.124057,9.41057e-05,0.483658,3.94701e-05,0.301581,0.261657,0.0686105,0.00395053,0.545655,0.438176,0.349112,0.391754,0.00159055,0.0531591,0.461541,0.00160821,0.382854,5.35254e-06,0.00448414,0.00289554,0.319747,0.136743,0.0498053,0.608127,0.282281,0.00293082,0.2536,0.246827,0.564333,0.00168296,0.387134,0.559969,0.358813,0.668972,0.0554837,0.493455,0.346636,0.00360135,0.348802,0.0280449,0.215342,0.447581,0.42505,0.254628,4.88736e-05,0.479347,0.416962,0.264955,0.378333,7.96957e-05,0.264038,0.22798,0.102495,8.78499e-05,0.263896,0.0446972,0.24452,0.329284,0.0321969,0.0947248,0.336551,0.210656,0.246234,0.211271,0.0439036,0.0394002,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.187728,0.231754,0.00317894,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,1.09244e-05,0.16188,0.23235,0.0469743,0.353147,7.66309e-06,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.000266472,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.00326229,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.0311922,0.095257,0.328852,0.332769,8.4285e-07,0.274403,0.0392261,0.0181825,0.248707,0.000654779,0.15156,0.287598,0.313858,0.223773,0.25788,5.76789e-05,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.0888526,0.355805,0.279739,0.108118,0.259901,0.000507733,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.000195446,0.332746,0.271338,0.032013,0.00571761,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.000297685,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.00739196,0.229571,0.359036,0.335984,0.171704,0.00010286,0.0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}}
}}

Revision as of 14:24, 19 October 2012


Full id: C2772_mesenchymal_Fibroblast_Cardiac_Smooth_Chondrocyte_Anulus_tenocyte



Phase1 CAGE Peaks

Hg19::chr4:114682288..114682309,-p5@CAMK2D
Hg19::chr4:114682310..114682325,-p6@CAMK2D
Hg19::chr4:114682326..114682356,-p2@CAMK2D
Hg19::chr4:114682364..114682379,-p3@CAMK2D


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
fibroblast1.77e-1276
multi fate stem cell8.42e-11427
somatic stem cell1.65e-09433
skin fibroblast4.83e-0923
muscle precursor cell4.91e-0858
myoblast4.91e-0858
multi-potent skeletal muscle stem cell4.91e-0858
stem cell5.02e-08441
muscle cell5.30e-0755
Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue7.37e-1173
paraxial mesoderm1.63e-1072
presumptive paraxial mesoderm1.63e-1072
somite1.92e-1071
presomitic mesoderm1.92e-1071
presumptive segmental plate1.92e-1071
dermomyotome1.92e-1071
trunk paraxial mesoderm1.92e-1071
muscle tissue7.39e-1064
musculature7.39e-1064
musculature of body7.39e-1064
musculoskeletal system2.75e-09167
skeletal muscle tissue2.89e-0962
striated muscle tissue2.89e-0962
myotome2.89e-0962
anatomical system7.39e-09624
mesoderm1.13e-08315
mesoderm-derived structure1.13e-08315
presumptive mesoderm1.13e-08315
anatomical group1.29e-08625
tissue2.16e-08773
primary circulatory organ2.19e-0827
epithelial vesicle3.14e-0878
multi-cellular organism1.64e-07656
multilaminar epithelium1.80e-0783
heart3.55e-0724
primitive heart tube3.55e-0724
primary heart field3.55e-0724
anterior lateral plate mesoderm3.55e-0724
heart tube3.55e-0724
heart primordium3.55e-0724
cardiac mesoderm3.55e-0724
cardiogenic plate3.55e-0724
heart rudiment3.55e-0724


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
CEBPB#105147.971147625824820.0002476385788090830.00268456773222356
CTBP2#1488462.71700033932816.45042639894877e-083.96513291747976e-06
NFKB1#479045.488063424193840.001102199566301980.00768955380795005
TAF1#687243.343046285745290.008005664898701650.0322994528453798



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.