Personal tools

Coexpression cluster:C1187: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 5: Line 5:
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.97e-18!115;UBERON:0000073!1.48e-13!94;UBERON:0001016!1.48e-13!94;UBERON:0005743!7.99e-13!86;UBERON:0001049!9.30e-13!57;UBERON:0005068!9.30e-13!57;UBERON:0006241!9.30e-13!57;UBERON:0007135!9.30e-13!57;UBERON:0003075!3.79e-12!86;UBERON:0007284!3.79e-12!86;UBERON:0001017!1.53e-11!82;UBERON:0003056!2.90e-11!61;UBERON:0002346!3.08e-11!90;UBERON:0003080!5.76e-11!42;UBERON:0002780!1.34e-10!41;UBERON:0001890!1.34e-10!41;UBERON:0006240!1.34e-10!41;UBERON:0002616!1.19e-09!59;UBERON:0000955!3.83e-09!69;UBERON:0006238!3.83e-09!69;UBERON:0002020!8.13e-09!34;UBERON:0003528!8.13e-09!34;UBERON:0001893!4.66e-08!34;UBERON:0002791!6.00e-08!33;UBERON:0001869!6.80e-08!32
|ontology_enrichment_uberon=UBERON:0007023!7.97e-18!115;UBERON:0000073!1.48e-13!94;UBERON:0001016!1.48e-13!94;UBERON:0005743!7.99e-13!86;UBERON:0001049!9.30e-13!57;UBERON:0005068!9.30e-13!57;UBERON:0006241!9.30e-13!57;UBERON:0007135!9.30e-13!57;UBERON:0003075!3.79e-12!86;UBERON:0007284!3.79e-12!86;UBERON:0001017!1.53e-11!82;UBERON:0003056!2.90e-11!61;UBERON:0002346!3.08e-11!90;UBERON:0003080!5.76e-11!42;UBERON:0002780!1.34e-10!41;UBERON:0001890!1.34e-10!41;UBERON:0006240!1.34e-10!41;UBERON:0002616!1.19e-09!59;UBERON:0000955!3.83e-09!69;UBERON:0006238!3.83e-09!69;UBERON:0002020!8.13e-09!34;UBERON:0003528!8.13e-09!34;UBERON:0001893!4.66e-08!34;UBERON:0002791!6.00e-08!33;UBERON:0001869!6.80e-08!32
|tfbs_overrepresentation=0.31043,0.131575,0.947389,0.107813,0.0963218,0.547045,0.0974871,0.713283,0.0746874,0.0589549,0.295561,0.448908,0.0135048,0.269614,0.313114,0.138515,0.0498069,0.214302,0.119001,0.0298564,0.0865129,0.282418,0.180923,0.20757,0.0943256,0.432377,0.105165,0.199011,0.0516907,0.204444,0.414424,0.00304605,0.0415685,0.42006,0.148393,0.186108,0.934067,0.097401,0.258596,0.148774,0.210798,0.0564873,0.296737,0.0825771,0.259708,0.0825288,0.0864669,0.0804706,0.0316035,0.0372624,0.323223,0.12188,0.156121,0.203677,0.403772,0.0873518,0.232986,0.427667,0.173296,0.0285418,0.0673274,0.314503,0.0301481,0.0150344,0.122724,0.113864,0.637,0.134457,0.189423,0.34721,0.305127,0.0119966,0.195543,0.25669,0.0173573,0.0394864,0.00185422,0.00507057,0.00369869,0.0168408,0.209062,0.451469,0.00480042,0.247724,0.19247,0.491847,0.0108639,0.421411,0.888138,0.0103419,0.18877,0.00650848,0.208559,0.107066,0.0188986,0.248084,0.871457,0.322402,0.203166,0.0401823,0.129026,0.00743578,0.050411,0.0843602,0.0209057,0.0929061,0.0117582,0.250565,0.304684,0.167061,0.375285,0.0775356,0.314757,0.0407805,0.220427,0.0769904,0.0468147,0.00846114,0.294794,0.184794,0.346582,0.431052,0.0492283,0.0190689,0.0268874,0.0766709,0.198942,0.034178,0.0184574,0.286955,0.133529,3.9117e-05,0.128445,0.0523619,0.0400263,0.0298795,0.011038,0.00807792,0.0754012,0.00920461,0.052339,0.00425011,0.00219127,0.326814,0.879733,0.154324,0.0251107,0.1856,0.0885156,0.0370447,0.406997,3.8323e-05,0.0798054,0.0609284,0.0968299,0.0351291,0.165818,0.453904,0.116496,0.0769293,0.122873,0.0017859,0.000232104,0.00656307,0.525489,0.246608,0.0909267,0.00422673,0.0916381,0.012162,0.370083,0.0476287,0.766596,0.121785,0.17666,0.197691,0.297301,0.373889,0.367859,0.0811784,0.332099,0.0380194,0.0627829,0.000223685,0.16364,0.000250224,0.0817441,0.0912436,0.18278,7.35817e-06,0.232364,0.085364,0.0382955,0.45461,0.243403,0.106408,0.0159389,0.135052,0.150784,0.237426,0.196091,0.135293,0.0704675,0.00965948,0.289872,0.503773,0.525644,0.0573911,0.102289,0.367697,0.103767,0.226759,0.260173,0.0324967,0.58295,0.0703658,0.341984,0.219863,0.140859,0.224003,0.300341,0.0970147,0.32693,0.0641653,0.163924,0.0405287,0.294471,0.0191515,0.135411,0.00044795,0.860233,0.313214,0.0949171,0.169481,0.209657,0.204086,0.106746,0.509502,0.340697,0.110275,0.0812749,0.63269,0.214704,0.01792,0.25057,0.00522664,0.0172605,0.241366,0.296754,0.0348288,0.332484,0.37985,0.380877,0.213951,0.0247506,0.333636,0.0294219,0.0982188,0.154888,0.869652,0.138561,0.0751959,0.340466,0.273737,0.0786852,0.00110427,0.179229,0.201771,0.00337673,0.16741,0.177325,0.141494,0.496492,0.748734,0.0194203,0.0865316,0.27777,0.337299,0.945764,0.971688,0.682134,0.855118,0.912027,0.737802,0.614575,0.408427,0.00596839,0.74825,0.297951,0.5782,0.467833,0.0153605,0.691446,0.0683894,0.106354,0.653093,0.170031,0.00932087,0.342602,0.693154,0.332445,0.6259,0.0131876,0.283193,0.0806417,0.723928,0.00273548,0.241288,0.0206944,0.142766,0.100365,0.765804,0.439013,0.523159,0.820271,0.294002,0.356647,0.78693,0.0320349,0.0075019,0.00172738,0.0699586,0.589017,0.445808,0.225057,0.172221,0.0443978,0.22091,0.326362,0.552809,0.163342,0.865425,0.358319,0.194259,0.445937,0.000505872,0.664607,0.866143,0.64314,0.0122018,0.544439,0.909661,0.959833,0.0407037,0.0261344,0.012861,0.261292,0.534084,0.16893,0.899187,0.485234,0.814166,0.821424,0.144423,0.537738,0.189123,0.0658527,0.14951,0.000811183,0.379192,0.62513,0.965193,0.332632,0.352637,0.263267,0.842267,0.846076,0.163285,0.437649,0.218504,0.764114,0.102102,3.8946e-05,0.124156,0.4435,0.874639,0.223746,0.00965229,0.0768885,0.77992,0.189961,0.236455,0.931576,0.532418,0.9786,0.375364,0.453428,0.248259,0.0154528,0.060642,0.311274,0.137608,0.20071,0.13684,0.241579,0.98961,0.246698,3.98834e-05,0.0529282,0.314229,0.667503,0.402503,0.0157838,0.0315444,0.057991,0.10531,0.291113,0.503499,0.286678,0.0249939,0.2811,0.00952102,0.0447915,0.625729,0.0555285,0.209856,0.170211,0.083253,0.0972203,0.184595,0.508647,0.278714,0.450384,0.34286,0.00939726,0.284394,0.180912,0.961929,0.102218,0.51876,0.704347,0.738461,0.0381311,0.252097,0.846682,0.180871,0.00580246,0.757775,0.820036,0.33353,0.470604,0.662621,0.0036988,0.387548,0.195754,0.133496,0.252578,0.898787,0.0794719,0.0370478,0.0811734,0.066121,0.340899,0.427426,0.901882,0.588029,0.15528,0.125135,0.392877,0.172615,0.129203,0.304883,0.445623,0.412193,0.744608,0.743378,0.0892376,0.00288147,0.54931,0.0986558,0.569749,0.000321256,0.0457431,0.0292356,0.525257,0.140425,0.673929,0.0412928,0.570618,0.535059,0.684902,0.105116,0.351863,0.00308883,0.0280136,0.00150494,0.00134853,0.00827138,0.00252848,0.00510948,0.00905448,0.0038661,0.275796,0.42369,0.394858,0.261362,0.112748,0.0178375,0.148755,0.0121654,0.00283178,0.114678,0.243744,0.398206,0.0440343,0.3861,0.00614903,0.405826,0.342943,0.000334512,0.363066,0.0829717,0.0705049,0.192669,0.208253,0.0260665,0.117649,0.232159,0.00107184,0.0111948,0.074071,0.298797,0.425775,0.0687597,0.00465119,0.10082,0.117938,0.421126,0.321571,0.176362,0.212715,0.334514,0.0386508,0.19886,0.00821347,0.539304,0.817594,0.291561,0.0337354,0.146629,0.426032,0.440859,0.177111,0.167984,0.0647522,0.0904963,0.00795414,0.0158273,0.126216,0.00463747,0.00318545,0.0883646,0.0324422,0.00997464,0.00206896,0.11039,0.361507,0.660283,0.0754745,0.632378,0.114847,0.00414749,0.000442414,0.361823,0.038021,0.000175997,0.0027379,0.506939,8.29768e-07,0.844302,0.305348,0.0883079,0.192275,0.123717,0.00608646,0.00527825,0.435034,0.388488,0.043326,0.689314,0.468189,0.545823,0.168686,0.35711,0.0174129,0.0814673,0.614081,0.311267,0.0501326,0.347601,0.297851,0.0204686,0.578705,0.187498,0.106912,0.207535,0.399867,0.283013,0.17144,0.236468,0.274647,0.00464089,0.933654,0.750867,0.1168,0.0253961,0.00662507,0.0100469,4.05563e-05,0.00169652,0.00608738,8.26461e-05,0.00084767,0.175877,0.956744,0.452369,0.435374,0.54926,0.25636,0.392755,0.366993,0.843094,0.12921,0.107541,0.688004,0.136306,0.362226,0.565792,0.158567,0.446426,0.551931,0.0810658,0.00405574,0.00118697,0.996492,0.998378,0.102432,0.0206565,0.234633,0.150144,0.235575,0.111506,0.209512,0.415762,0.000896234,0.00552932,0.238509,0.156356,0.450242,0.322099,0.0857464,0.282499,0.101873,0.121306,0.0332472,0.0222954,0.0730406,0.00237982,0.116879,0.128341,0.463619,0.168391,0.545636,0.320047,0.397073,0.437057,0.221207,0.603174,0.358,0.621995,0.318595,0.0103184,0.390753,0.312917,0.805801,0.326484,0.15977,0.201434,0.134947,0.00611607,0.0565162,0.212636,0.325012,0.353123,0.00177996,0.0472939,0.453507,0.491263,0.00881004,0.035987,0.184894,0.609179,0.244347,0.243363,0.0848007,0.361244,0.207462,0.0360514,0.487422,0.29768,0.217499,0.500934,0.0275524,0.244195,0.0586175,0.0694648,0.198885,0.608664,0.347052,0.386025,0.1797,0.379465,0.327304,0.217315,0.812383,0.132491,0.48467,0.367752,0.113563,0.458334,0.344739,0.895348,0.0821811,0.71056,0.279549,0.0984834,0.284421,0.71736,0.658832,0.1643,0.125046,0.0245454,0.547863,0.391162,0.0952538,0.371825,0.750889,0.401507,0.692805,0.648881,0.703424,0.103532,0.86822,0.910041,0.147508,0.949628,0.684866,0.790371,0.802111,0.0499894,0.515017,0.99232,0.991631,0.0232232,0.50853,0.656157,0.107763,0.0448062,0.226936,0.558605,0.587435,0.189803,0.341975,0.765292,0.547149,0.592518,0.448065,0.615729,0.771117,0.501908,0.74852,0.0284264,0.864643,0.685599,0.954834,0.931591,0.337191,0.834663,0.694783,0.474713,0.976385,0.297799,0.873084,0.779967,0.692633,0.959499,0.858681,0.411785,0.40673,0.101625,0.565657,0.499305,0.726141,0.632958,0.676266,0.327011,0.299176,0.710278,0.210121,0.585578,0.272487,0.341296,0.457524,0.00356216,0.541728,0.854621,0.585566,0.373172,0.538803,0.970782,0.654029,0.125952,0.241641,0.230258,0.917146,0.252282,0.88908,0.00117491,0.821879,0.890974,0.536712,0.117262,0.358039,0.132914,0.425138,0.954715,0.599651,0.41419,0.0543219,0.0054598,0.484505,0.346938,0.015499,0.183851,0.0608535,0.0693025,0.0108427,0.0157798,0.664218,0.250792,0.706724,0.654039,0.532798,0.685486,0.651111,0.466416,0.411899,0.525367,0.667,0.748565,0.635414,0.528332,0.906271,0.573415,0.474724,0.661532,0.210935,0.570287,0.797742,0.68023,0.808962,0.000665218,0.311129,0.760368,0.805909,0.440345,0.809866,0.400622,0.391073,0.766374,0.632822,0.21176,0.420733,0.0012482,0.855535,0.440278,0.333846,0.525188,0.0938213,0.52794,0.10627,0.780554,0.278413,0.0171218,0.402066,0.887664,0.31638,0.070317,0.826815,2.65294e-05,0.679978,0.415214,0.364157,0.172412,0.0413582,0.0172795,0.0769041,0.387804,0.155446,0.385339,0.159832,0.000878985,0.338978,0.390233,0.339879,0.114722,0.41967,0.197678,0.208523,0.34551,0.0051529,0.670197,0.497662,0.418843,0.162419,0.0787267,0.394729,0.441472,0.118183,0.622992,0.580249,3.03912e-05,0.403472,0.382758,0.264429,0.0960556,0.0744027,0.204325,0.265849,0.370442,0.451398,0.533438,0.188364,0.279598,0.420279,0.143312,0.443868,0.011877,0.104304,0.163945,0.00297106,0.307495,0.455626,0.0650142,0.124108,0.350305,0.0875262,0.147486,0.117583,0.103076,0.518238,0.40865,0.634608,0.324846,0.25829,0.215261,0.235004,0.133496,0.433115,0.331422,0.115587,0.397558,0.266168,0.504119,0.57634,0.371725,0.334024,0.500457,0.316975,0.0203584,0.26559,0.0828289,0.00149182,0.000786165,0.155054,0.15862,0.412407,0.42955,0.0178435,0.300222,0.0144202,0.487504,0.249956,0.022473,0.482721,0.35808,0.0969253,0.296254,0.0939442,0.473667,0.000755196,0.279523,0.499937,0.444635,0.0728075,0.0765707,0.00187952,0.409573,0.579867,0.536787,0.0206478,0.181464,0.40945,0.231548,0.120636,0.121001,0.0568736,0.172653,0.0924531,0.120918,0.593272,0.507382,0.425328,0.384398,0.462521,0.387627,0.179489,0.00194836,0.143317,0.0376847,0.14273,0.0280364,0.147968,0.168955,0.274981,0.236422,0.0999117,0.149301,0.196723,0.0836477,0.287028,0.413461,0.197757,0.545381,0.0186554,0.299959,0.509613,0.498355,0.406059,0.122646,0.56256,0.00526281,0.366448,0.540845,0.511559,0.280842,0.00839846,0.416632,0.0958507,0.18724,0.00397643,0.233968,0.249647,0.43669,0.119023,0.248584,0.397145,0.390152,0.00805113,0.540199,0.488863,0.342785,0.447064,0.20487,0.603936,0.120919,0.41929,0.209566,0.189123,0.0129295,0.0724476,0.332105,0.522124,0.158122,0.168501,0.0262058,0.117762,0.363335,0.329186,0.111136,0.148874,0.00228043,0.0890644
}}
}}

Revision as of 16:59, 8 August 2012


Full id: C1187_anaplastic_gastric_small_carcinoid_acute_retinoblastoma_merkel



Phase1 CAGE Peaks

Hg19::chr13:72166623..72166627,-p@chr13:72166623..72166627
-
Hg19::chr13:72322304..72322306,-p@chr13:72322304..72322306
-
Hg19::chr13:72358093..72358097,-p@chr13:72358093..72358097
-
Hg19::chr13:72375972..72375975,-p@chr13:72375972..72375975
-
Hg19::chr13:72381549..72381552,-p@chr13:72381549..72381552
-
Hg19::chr13:72394234..72394237,-p@chr13:72394234..72394237
-
Hg19::chr13:72436036..72436040,-p@chr13:72436036..72436040
-


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism7.97e-18115
regional part of nervous system1.48e-1394
nervous system1.48e-1394
neural tube9.30e-1357
neural rod9.30e-1357
future spinal cord9.30e-1357
neural keel9.30e-1357
neural plate3.79e-1286
presumptive neural plate3.79e-1286
central nervous system1.53e-1182
pre-chordal neural plate2.90e-1161
neurectoderm3.08e-1190
anterior neural tube5.76e-1142
regional part of forebrain1.34e-1041
forebrain1.34e-1041
future forebrain1.34e-1041
regional part of brain1.19e-0959
brain3.83e-0969
future brain3.83e-0969
gray matter8.13e-0934
brain grey matter8.13e-0934
telencephalon4.66e-0834
regional part of telencephalon6.00e-0833
cerebral hemisphere6.80e-0832


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.