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Coexpression cluster:C2750: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.51e-37!112;UBERON:0002390!1.04e-32!102;UBERON:0003061!1.04e-32!102;UBERON:0003081!8.21e-30!216;UBERON:0007023!7.97e-29!115;UBERON:0002371!1.39e-28!80;UBERON:0002405!1.83e-27!115;UBERON:0001474!3.31e-25!86;UBERON:0004765!6.21e-20!101;UBERON:0001434!6.21e-20!101;UBERON:0001986!4.70e-16!18;UBERON:0004638!4.70e-16!18;UBERON:0004852!4.70e-16!18;UBERON:0000487!1.69e-11!22;UBERON:0006914!8.17e-10!25;UBERON:0003915!3.21e-09!9;UBERON:0004700!3.21e-09!9;UBERON:0001917!3.21e-09!9;UBERON:0001009!4.36e-09!113;UBERON:0004535!1.78e-08!110;UBERON:0002204!1.43e-07!167;UBERON:0000479!1.96e-07!787;UBERON:0000055!6.33e-07!69;UBERON:0001049!8.13e-07!57;UBERON:0005068!8.13e-07!57;UBERON:0006241!8.13e-07!57;UBERON:0007135!8.13e-07!57
|ontology_enrichment_uberon=UBERON:0002193!1.51e-37!112;UBERON:0002390!1.04e-32!102;UBERON:0003061!1.04e-32!102;UBERON:0003081!8.21e-30!216;UBERON:0007023!7.97e-29!115;UBERON:0002371!1.39e-28!80;UBERON:0002405!1.83e-27!115;UBERON:0001474!3.31e-25!86;UBERON:0004765!6.21e-20!101;UBERON:0001434!6.21e-20!101;UBERON:0001986!4.70e-16!18;UBERON:0004638!4.70e-16!18;UBERON:0004852!4.70e-16!18;UBERON:0000487!1.69e-11!22;UBERON:0006914!8.17e-10!25;UBERON:0003915!3.21e-09!9;UBERON:0004700!3.21e-09!9;UBERON:0001917!3.21e-09!9;UBERON:0001009!4.36e-09!113;UBERON:0004535!1.78e-08!110;UBERON:0002204!1.43e-07!167;UBERON:0000479!1.96e-07!787;UBERON:0000055!6.33e-07!69;UBERON:0001049!8.13e-07!57;UBERON:0005068!8.13e-07!57;UBERON:0006241!8.13e-07!57;UBERON:0007135!8.13e-07!57
|tf_chipseq_enrich=BATF#10538;4:24.3578017923036:2.83869198020713e-06:9.79095613344956e-05!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268401053676233!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195154253622569!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000723500986983916!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000744400002154293!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486051605374017!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249736738674354!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322907209035454
|tfbs_overrepresentation=0.191353,0.0774498,0.814139,0.0631091,0.257053,0.363996,0.0569281,0.00615604,0.043387,0.0341265,0.181435,0.0463459,0.0323727,0.164339,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,4.63254e-05,0.107781,0.00809151,0.0550418,0.276459,0.00405868,0.119094,0.186914,0.122514,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,0.788552,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.145553,3.1982e-05,0.19996,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.273035,0.103044,0.138225,0.0390464,0.194086,0.142115,0.0999599,0.0720888,0.0667453,0.439574,0.0792005,0.113084,0.216289,0.470097,0.0892037,0.116917,1.0129e-06,0.00995563,0.0227583,0.126543,3.36951e-05,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.150119,0.368178,0.320801,0.0848546,0.268505,0.713984,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.690341,0.199405,0.121709,0.347653,0.0759036,0.350158,0.0181842,0.0491142,0.280878,0.0541957,0.0883058,0.423154,0.187509,0.34189,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.275495,0.182323,0.112709,0.134107,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,3.62687e-08,0.164103,1.99718e-05,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,0.202388,0.701894,0.0913381,0.129544,0.110696,0.0515825,1.07831e-06,0.0366263,0.0186533,0.233377,0.0352845,0.0565357,0.0124479,0.0984158,0.29227,0.0683304,0.00101483,0.291455,0.124982,0.152417,0.192028,3.48282e-07,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.000164242,0.179282,0.0103372,0.0715212,0.00573076,0.118265,0.182591,0.234755,0.230552,0.0472274,0.00172168,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.241581,0.160458,0.292792,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.0616625,0.346995,0.197158,0.265132,0.230439,0.0606832,0.136664,0.158184,0.147626,0.393313,0.00208748,0.21271,0.132273,0.0830988,0.134907,0.184613,0.462724,0.202467,0.208718,0.0972471,0.165147,0.180711,0.112956,0.0797807,0.0790532,0.675167,0.476758,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.0204686,0.128998,0.00619501,0.151958,0.178155,0.107176,0.146021,0.463127,0.15291,0.206234,0.238926,0.239646,0.128521,0.1286,0.207017,0.14037,0.259646,0.0916845,0.687863,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.00589547,0.106727,0.12083,0.154253,0.0993998,0.352707,0.0834863,0.324356,0.00867491,0.00673033,0.0504034,0.169684,0.114577,0.810881,0.603871,0.73998,0.3024,0.672445,0.888682,0.420045,0.73391,0.332539,0.545329,0.464128,0.389374,0.594055,0.414547,0.489273,0.413223,0.639461,0.720642,0.34505,0.369161,0.500422,0.49089,0.687176,0.341822,0.241524,0.45167,0.234628,0.520726,0.143893,0.41477,0.279946,0.524104,0.467825,0.563725,0.751064,0.632838,0.624969,0.460819,0.161502,0.586668,0.0073977,0.0703732,0.380582,0.583749,0.398372,0.286293,0.606558,0.708425,0.359128,0.395864,0.683133,0.368633,0.547291,0.682118,0.512763,0.369971,0.578349,0.537928,0.464342,0.683088,0.131933,4.13292e-07,0.804772,0.668093,0.840703,0.349116,0.302142,0.239545,0.432689,0.640367,0.343881,0.730486,0.606382,0.617741,0.0774588,0.316925,0.356561,0.573659,0.211506,0.0883859,4.0315e-06,0.238465,0.122819,0.853221,0.6873,0.508325,0.773224,0.651927,0.656755,0.54723,0.280307,0.393583,0.212518,0.0596868,0.0984075,0.293026,0.753513,0.694744,0.605423,0.372182,0.429205,0.578951,0.365653,0.41035,0.784024,3.96422e-07,0.888839,0.525923,0.291917,0.421082,0.00338934,0.202782,0.672876,0.517933,0.0124357,0.517001,0.620475,0.926442,0.419676,0.0189509,0.189182,0.477589,0.46699,0.546448,0.560187,0.321282,0.021087,0.0616078,0.178485,0.329745,0.175552,0.129238,0.651295,0.370995,0.360161,0.429696,0.386216,0.385297,0.706685,0.606408,0.627185,0.360203,0.333725,0.00323929,0.289666,0.500627,0.513045,0.452694,0.565545,0.845507,0.0387162,0.629795,0.0543569,0.0427118,0.341771,0.424526,0.657528,0.356381,0.184395,0.55524,0.624689,0.206945,0.304719,0.00378814,0.296994,0.244339,0.117049,0.0786167,7.95194e-05,0.144936,0.433821,0.64428,0.436806,0.576549,0.00550983,0.744662,0.734628,0.397546,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.000411464,0.261868,0.541583,0.540322,0.247151,0.146385,0.365815,3.33332e-05,0.382413,0.164977,0.175633,0.139918,0.34669,0.0828344,0.4729,0.0238089,0.383126,0.354433,0.0294482,0.0614918,0.000128965,0.149782,0.136923,0.118103,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.249506,0.432751,0.0660736,0.108971,0.0879235,0.235214,0.000576697,0.28124,0.417003,0.251882,5.39512e-08,0.243319,0.0637178,0.257309,0.500692,0.166608,0.227224,0.238082,0.219023,0.115115,0.124916,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.224626,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.002785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67,0.357807,0.621787,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.00269603,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.00357445,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.000773597,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.00601454,0.0303023,0.419621,0.191914,0.00120447,0.216557,0.182956,0.116818,0.0139335,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.833813,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.285695,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.0278061,0.960445,0.974549,0.00388363,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.000332882,0.22302,0.137423,0.284016,1.48526e-06,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.000213802,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.000681832,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.0277041,0.124417,0.335582,0.317428,0.182843,0.000413166,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.0466753,0.502211,0.0489167,0.649813,0.537932,0.0247432,0.523209,0.189126,0.25423,0.490559,0.45013,0.500698,0.472542,0.685908,0.747471,0.529642,0.818701,0.483077,0.590496,0.603763,0.541914,0.627201,0.938109,0.934991,0.00523185,0.622694,0.722684,0.478691,0.360199,0.608176,0.657141,0.824761,0.365494,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.0458249,0.310552,0.865054,0.483764,0.829658,0.453065,6.39764e-09,0.843495,0.748403,0.598945,0.882403,0.464001,0.871271,0.579004,0.870272,0.839946,0.860705,0.261575,0.257956,0.264245,0.379063,0.326516,0.0069676,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.86719,0.721266,0.50338,0.620526,0.404625,0.416164,0.0187136,0.715362,0.479581,0.0181348,0.884725,0.642173,0.284496,0.000103689,0.00087777,0.00164085,0.829402,0.684899,0.263302,0.552023,0.180735,0.775168,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.741477,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.00431644,0.0498053,0.608127,0.0442299,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.668972,0.574252,0.00520796,0.000975164,0.457747,0.348802,0.476541,0.0118751,0.447581,0.0187686,0.254628,0.713293,0.479347,0.416962,0.632833,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.002982,0.329284,0.242783,0.0947248,0.336551,0.210656,0.000212417,0.211271,0.000381355,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.0340704,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.0238089,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.0662546,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.042497,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.0612213,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.0452813,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.0206568,0.102645,0.0539258,0.0709978,0.401939,0.00817441,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,1.70389e-05,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.0123861,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.000524161,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.00304766,0.0011123,0.0737175,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,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}}
}}

Revision as of 14:19, 5 September 2012


Full id: C2750_Endothelial_immature_Macrophage_Mast_CD34_Lymphatic_CD14



Phase1 CAGE Peaks

Hg19::chr3:69402726..69402747,-p6@FRMD4B
Hg19::chr3:69402751..69402762,-p17@FRMD4B
Hg19::chr3:69402773..69402820,-p5@FRMD4B
Hg19::chr3:69402828..69402852,-p8@FRMD4B


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
myeloid leukocyte2.93e-3476
myeloid cell3.46e-34112
common myeloid progenitor3.46e-34112
granulocyte monocyte progenitor cell1.55e-3271
myeloid lineage restricted progenitor cell7.23e-2970
macrophage dendritic cell progenitor2.77e-2865
CD14-positive, CD16-negative classical monocyte1.49e-2742
hematopoietic stem cell1.12e-26172
angioblastic mesenchymal cell1.12e-26172
monopoietic cell1.17e-2663
monocyte1.17e-2663
monoblast1.17e-2663
promonocyte1.17e-2663
hematopoietic cell2.85e-25182
classical monocyte3.28e-2545
leukocyte4.05e-24140
hematopoietic oligopotent progenitor cell5.06e-24165
hematopoietic multipotent progenitor cell5.06e-24165
endothelial cell1.19e-2335
endothelial cell of vascular tree7.78e-2124
hematopoietic lineage restricted progenitor cell1.39e-18124
meso-epithelial cell3.48e-1644
nongranular leukocyte3.70e-16119
blood vessel endothelial cell4.70e-1618
embryonic blood vessel endothelial progenitor cell4.70e-1618
endothelial cell of artery3.21e-099
lining cell3.40e-0957
barrier cell3.40e-0957
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.51e-37112
hematopoietic system1.04e-32102
blood island1.04e-32102
lateral plate mesoderm8.21e-30216
adult organism7.97e-29115
bone marrow1.39e-2880
immune system1.83e-27115
bone element3.31e-2586
skeletal element6.21e-20101
skeletal system6.21e-20101
endothelium4.70e-1618
blood vessel endothelium4.70e-1618
cardiovascular system endothelium4.70e-1618
simple squamous epithelium1.69e-1122
squamous epithelium8.17e-1025
endothelial tube3.21e-099
arterial system endothelium3.21e-099
endothelium of artery3.21e-099
circulatory system4.36e-09113
cardiovascular system1.78e-08110
musculoskeletal system1.43e-07167
tissue1.96e-07787
vessel6.33e-0769
neural tube8.13e-0757
neural rod8.13e-0757
future spinal cord8.13e-0757
neural keel8.13e-0757


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
BATF#10538424.35780179230362.83869198020713e-069.79095613344956e-05
CEBPB#105147.971147625824820.0002476385788090830.00268401053676233
FOS#235348.99795530889440.0001525147711168630.00195154253622569
GATA2#2624412.7449317335543.78864877853583e-050.000723500986983916
JUN#3725412.51282919233634.07770316866756e-050.000744400002154293
MAX#414946.452555509007120.0005767613195645490.00486051605374017
SPI1#668848.204323508522730.000220661881527680.00249736738674354
TAF1#687243.343046285745290.008005664898701650.0322907209035454



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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