Personal tools

Coexpression cluster:C3854: 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:0003914!1.47e-19!118;UBERON:0001637!3.26e-14!42;UBERON:0003509!3.26e-14!42;UBERON:0004572!3.26e-14!42;UBERON:0000490!2.34e-13!138;UBERON:0004872!4.73e-13!84;UBERON:0004573!2.95e-12!33;UBERON:0004571!2.95e-12!33;UBERON:0001981!3.75e-12!60;UBERON:0007500!3.75e-12!60;UBERON:0004537!3.75e-12!60;UBERON:0006965!3.75e-12!60;UBERON:0000926!4.74e-12!448;UBERON:0004120!4.74e-12!448;UBERON:0006603!4.74e-12!448;UBERON:0001009!1.67e-11!113;UBERON:0000055!2.02e-11!69;UBERON:0002049!4.94e-11!79;UBERON:0007798!4.94e-11!79;UBERON:0004535!1.36e-10!110;UBERON:0004111!1.47e-10!241;UBERON:0005256!2.01e-10!143;UBERON:0002100!2.54e-10!216;UBERON:0002385!1.46e-09!63;UBERON:0001015!1.46e-09!63;UBERON:0000383!1.46e-09!63;UBERON:0001134!3.52e-09!61;UBERON:0002036!3.52e-09!61;UBERON:0003082!3.52e-09!61;UBERON:0000468!1.11e-08!659;UBERON:0000467!1.89e-08!625;UBERON:0000480!3.15e-08!626;UBERON:0003064!3.98e-08!37;UBERON:0000477!4.42e-08!286;UBERON:0003103!7.30e-08!69;UBERON:0003104!7.71e-08!238;UBERON:0009142!7.71e-08!238;UBERON:0000025!1.51e-07!194;UBERON:0003081!2.74e-07!216
|ontology_enrichment_uberon=UBERON:0003914!1.47e-19!118;UBERON:0001637!3.26e-14!42;UBERON:0003509!3.26e-14!42;UBERON:0004572!3.26e-14!42;UBERON:0000490!2.34e-13!138;UBERON:0004872!4.73e-13!84;UBERON:0004573!2.95e-12!33;UBERON:0004571!2.95e-12!33;UBERON:0001981!3.75e-12!60;UBERON:0007500!3.75e-12!60;UBERON:0004537!3.75e-12!60;UBERON:0006965!3.75e-12!60;UBERON:0000926!4.74e-12!448;UBERON:0004120!4.74e-12!448;UBERON:0006603!4.74e-12!448;UBERON:0001009!1.67e-11!113;UBERON:0000055!2.02e-11!69;UBERON:0002049!4.94e-11!79;UBERON:0007798!4.94e-11!79;UBERON:0004535!1.36e-10!110;UBERON:0004111!1.47e-10!241;UBERON:0005256!2.01e-10!143;UBERON:0002100!2.54e-10!216;UBERON:0002385!1.46e-09!63;UBERON:0001015!1.46e-09!63;UBERON:0000383!1.46e-09!63;UBERON:0001134!3.52e-09!61;UBERON:0002036!3.52e-09!61;UBERON:0003082!3.52e-09!61;UBERON:0000468!1.11e-08!659;UBERON:0000467!1.89e-08!625;UBERON:0000480!3.15e-08!626;UBERON:0003064!3.98e-08!37;UBERON:0000477!4.42e-08!286;UBERON:0003103!7.30e-08!69;UBERON:0003104!7.71e-08!238;UBERON:0009142!7.71e-08!238;UBERON:0000025!1.51e-07!194;UBERON:0003081!2.74e-07!216
|tfbs_overrepresentation=0.147255,0.0586687,0.35968,0.0477154,0.00156205,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.00153794,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.241734,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0594776,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.0085119,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.12972,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.0178773,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.0128655,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.0219021,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.131316,0.00102762,0.635872,0.20128,0.0986134,0.489965,0.0638737,0.629514,0.261553,0.000368869,0.373681,2.59595e-06,0.49143,0.330703,0.395854,0.329568,0.53472,0.248224,0.271958,0.292154,0.405773,0.0921263,0.217139,0.230901,0.187251,0.362792,0.181715,0.10624,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.0407001,0.520763,0.370782,0.415647,0.484505,0.00335333,0.00445889,0.301787,0.481778,0.0565541,0.223503,0.503224,0.603208,0.283727,0.314747,0.21363,0.291709,0.0225637,0.576651,0.416816,0.292835,0.476744,0.0210941,0.373868,0.57762,0.608919,0.18237,0.706298,0.513427,0.747852,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.258117,0.000781971,0.163222,0.169228,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.421596,0.581837,0.412837,0.00102656,0.188159,0.551561,0.448039,0.00208206,0.312808,0.032738,0.0451077,0.0747529,0.229003,0.650179,0.223844,0.50215,0.294698,0.000933193,0.138202,0.0465597,0.327108,0.319027,0.278044,0.229008,0.428671,0.228096,0.336314,0.0209597,0.15631,0.567452,0.421464,0.48267,0.104399,0.165111,0.311758,0.335105,0.144809,0.145539,0.000152461,0.0818086,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.18767,0.293698,0.0450006,0.343734,0.306556,0.305777,0.06617,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.0175765,0.363685,0.464871,0.753577,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.0014397,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.0688327,0.182325,0.34988,0.475069,0.404569,0.273024,0.0793778,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.00427764,0.0627924,0.381386,0.0179103,0.303939,0.0434097,0.390395,0.0464827,0.00093131,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.0205132,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.0694567,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.00615421,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.00502301,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.000356768,0.739716,0.0232393,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.43617,0.76084,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.0362615,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.0743925,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.0785808,0.120614,0.0973145,0.231447,0.18653,0.43956,0.37006,0.42622,0.448797,0.0209277,0.396996,0.36145,0.0160226,0.0129,0.216033,0.00417723,2.80983e-05,0.722159,0.390366,0.48809,0.50058,0.000353311,0.169835,0.616975,0.871256,0.227104,0.518585,0.250246,0.38649,0.284625,0.0344717,0.55194,0.144318,0.28907,0.164197,0.128922,0.287881,0.574635,0.000566617,0.336276,0.468444,0.258219,0.446557,0.243383,0.0186777,0.000165723,0.73485,0.683217,0.161598,0.405056,0.021206,0.150692,0.21803,0.37357,0.200632,0.477353,0.069689,0.160298,0.43491,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.0851996,0.156104,0.141318,0.411941,0.0961477,0.314438,0.0720718,0.163828,0.230581,0.120226,0.28424,0.000219142,0.314429,0.181415,0.282286,0.0674279,0.00047615,0.408413,0.0374737,0.322213,0.0931134,0.33942,0.61031,0.387276,0.522605,0.221908,0.00800402,0.222037,0.416621,0.416292,0.000461257,0.734551,0.215157,0.204817,0.122646,0.0101228,0.673493,0.000885521,0.0210039,0.0833851,0.316453,0.0289164,0.175199,0.0628556,0.373557,0.523625,0.408861,0.0111982,0.178743,0.39088,0.363192,0.236011,0.203486,0.00428131,0.0123025,0.4466,0.0704514,0.275347,0.019895,3.99422e-05,0.241132,0.371414,0.30666,0.303709,0.15059,0.0135408,0.508064,0.00324315,0.383276,0.457886,0.000798597,0.220231,0.509064,0.196976,0.00136659,0.463751,0.601877,0.307334,0.459728,0.0048173,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.00444763,0.359231,0.339729,0.00151397,0.0690807,0.387069,0.332774,0.0406989,0.299887,0.266492,9.6965e-05,0.17639,0.0779009,0.00446098,0.205298,0.0337138,0.0192444,0.036838,0.188263,0.0719199,0.264884,0.162568,0.19104,0.000822975,0.0260582,0.208013,0.00418416,0.00469907,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.0211771,0.0186488,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.0335483,0.222339,0.0673329,0.20847,0.0391817,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.00361981,0.30793,0.180606,0.159884,0.0363723,0.150733,0.0254879,0.123917,0.184317,0.0183464,0.0723291,0.0367308,0.261744,0.203781,0.21382,0.0232077,0.141867,0.0199603,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.0269005,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.00339727,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.00206474,0.0271615,0.11528,0.194982,0.190993,0.0440463,0.283218,0.0032012,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.056548,0.171683,0.000758145,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 19:30, 8 August 2012


Full id: C3854_anaplastic_Cardiac_Mesothelial_mesothelioma_mesenchymal_Smooth_squamous



Phase1 CAGE Peaks

Hg19::chr1:12679045..12679065,-p@chr1:12679045..12679065
-
Hg19::chr1:12679075..12679086,-p@chr1:12679075..12679086
-
Hg19::chr1:12679100..12679121,-p@chr1:12679100..12679121
-


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
epithelial tube1.47e-19118
artery3.26e-1442
arterial blood vessel3.26e-1442
arterial system3.26e-1442
unilaminar epithelium2.34e-13138
splanchnic layer of lateral plate mesoderm4.73e-1384
systemic artery2.95e-1233
systemic arterial system2.95e-1233
blood vessel3.75e-1260
epithelial tube open at both ends3.75e-1260
blood vasculature3.75e-1260
vascular cord3.75e-1260
mesoderm4.74e-12448
mesoderm-derived structure4.74e-12448
presumptive mesoderm4.74e-12448
circulatory system1.67e-11113
vessel2.02e-1169
vasculature4.94e-1179
vascular system4.94e-1179
cardiovascular system1.36e-10110
anatomical conduit1.47e-10241
trunk mesenchyme2.01e-10143
trunk2.54e-10216
muscle tissue1.46e-0963
musculature1.46e-0963
musculature of body1.46e-0963
skeletal muscle tissue3.52e-0961
striated muscle tissue3.52e-0961
myotome3.52e-0961
multi-cellular organism1.11e-08659
anatomical system1.89e-08625
anatomical group3.15e-08626
intermediate mesoderm3.98e-0837
anatomical cluster4.42e-08286
compound organ7.30e-0869
mesenchyme7.71e-08238
entire embryonic mesenchyme7.71e-08238
tube1.51e-07194
lateral plate mesoderm2.74e-07216


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.