Personal tools

Coexpression cluster:C4288: 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:0003102!1.90e-13!95;UBERON:0000926!7.74e-12!448;UBERON:0004120!7.74e-12!448;UBERON:0006603!7.74e-12!448;UBERON:0000468!8.20e-11!659;UBERON:0002199!9.78e-10!45;UBERON:0002416!9.78e-10!45;UBERON:0004872!1.59e-09!84;UBERON:0000914!2.93e-09!83;UBERON:0002329!2.93e-09!83;UBERON:0003077!2.93e-09!83;UBERON:0003059!2.93e-09!83;UBERON:0007282!2.93e-09!83;UBERON:0009618!2.93e-09!83;UBERON:0007285!2.93e-09!83;UBERON:0000486!6.61e-09!82;UBERON:0002097!7.06e-09!40;UBERON:0000467!2.21e-08!625;UBERON:0002100!2.57e-08!216;UBERON:0000480!3.82e-08!626;UBERON:0004290!5.06e-08!70;UBERON:0004923!7.36e-08!57;UBERON:0002049!1.08e-07!79;UBERON:0007798!1.08e-07!79;UBERON:0001134!2.76e-07!61;UBERON:0002036!2.76e-07!61;UBERON:0003082!2.76e-07!61;UBERON:0002385!3.42e-07!63;UBERON:0001015!3.42e-07!63;UBERON:0000383!3.42e-07!63;UBERON:0005256!4.29e-07!143;UBERON:0001637!4.74e-07!42;UBERON:0003509!4.74e-07!42;UBERON:0004572!4.74e-07!42;UBERON:0001981!5.92e-07!60;UBERON:0007500!5.92e-07!60;UBERON:0004537!5.92e-07!60;UBERON:0006965!5.92e-07!60;UBERON:0000055!6.56e-07!69;UBERON:0005631!8.52e-07!14;UBERON:0000158!8.52e-07!14
|ontology_enrichment_uberon=UBERON:0003102!1.90e-13!95;UBERON:0000926!7.74e-12!448;UBERON:0004120!7.74e-12!448;UBERON:0006603!7.74e-12!448;UBERON:0000468!8.20e-11!659;UBERON:0002199!9.78e-10!45;UBERON:0002416!9.78e-10!45;UBERON:0004872!1.59e-09!84;UBERON:0000914!2.93e-09!83;UBERON:0002329!2.93e-09!83;UBERON:0003077!2.93e-09!83;UBERON:0003059!2.93e-09!83;UBERON:0007282!2.93e-09!83;UBERON:0009618!2.93e-09!83;UBERON:0007285!2.93e-09!83;UBERON:0000486!6.61e-09!82;UBERON:0002097!7.06e-09!40;UBERON:0000467!2.21e-08!625;UBERON:0002100!2.57e-08!216;UBERON:0000480!3.82e-08!626;UBERON:0004290!5.06e-08!70;UBERON:0004923!7.36e-08!57;UBERON:0002049!1.08e-07!79;UBERON:0007798!1.08e-07!79;UBERON:0001134!2.76e-07!61;UBERON:0002036!2.76e-07!61;UBERON:0003082!2.76e-07!61;UBERON:0002385!3.42e-07!63;UBERON:0001015!3.42e-07!63;UBERON:0000383!3.42e-07!63;UBERON:0005256!4.29e-07!143;UBERON:0001637!4.74e-07!42;UBERON:0003509!4.74e-07!42;UBERON:0004572!4.74e-07!42;UBERON:0001981!5.92e-07!60;UBERON:0007500!5.92e-07!60;UBERON:0004537!5.92e-07!60;UBERON:0006965!5.92e-07!60;UBERON:0000055!6.56e-07!69;UBERON:0005631!8.52e-07!14;UBERON:0000158!8.52e-07!14
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.0460856,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.00829112,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.00130254,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.0236364,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.324808,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.0125303,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.0347684,0.064341,0.209032,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.00407722,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.00428542,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,5.75739e-05,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.00549554,0.14193,0.37245,0.15606,0.0137227,0.0738599,0.126611,0.0101199,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.119261,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.451377,0.635872,0.563047,0.517782,0.0853552,0.335423,0.261644,0.261553,0.118991,0.373681,0.309233,0.49143,0.330703,0.395854,0.061507,0.0078057,0.248224,0.271958,0.292154,0.405773,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.0186051,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.608919,0.18237,0.706298,0.0310069,0.747852,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.0389686,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.0641718,0.762864,0.0583074,0.412837,0.305671,0.546839,0.551561,0.00324632,0.218623,0.312808,0.117923,0.0451077,0.0747529,0.229003,0.650179,0.223844,0.50215,0.294698,0.0671437,5.45446e-06,0.0465597,0.327108,0.319027,0.278044,0.490301,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.165111,0.135248,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.18767,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.169823,0.284629,0.262537,0.359455,0.226257,0.405955,0.102469,0.363685,0.464871,0.753577,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.262389,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.0434097,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.0205132,0.132201,2.80029e-06,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.0377931,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0791124,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,2.61649e-06,2.79364e-05,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.153605,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.0465298,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.43617,0.519327,0.206454,0.218192,0.108277,0.0673484,0.00613985,0.0494066,0.0958493,0.00171529,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.00921075,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.000415994,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.000797393,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,1.47161e-09,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.0364628,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.161789,0.0590944,0.247324,0.0169521,0.218229,0.231073,0.0020598,0.0743925,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.000247895,0.36927,0.0227305,0.407369,0.231447,0.18653,0.43956,0.37006,0.42622,0.448797,0.197484,0.0919774,0.36145,0.406019,0.381071,0.580441,0.276075,0.432035,0.722159,0.390366,0.48809,0.50058,0.443185,0.169835,0.616975,0.151996,0.227104,0.518585,0.617852,0.38649,0.284625,0.0344717,0.55194,0.729153,0.0465139,0.164197,0.462688,0.287881,0.574635,0.0283889,0.336276,0.468444,0.258219,0.446557,0.243383,0.0659137,0.0889613,0.73485,0.029557,0.161598,0.751174,0.644754,0.496032,0.799185,0.37357,0.0704414,0.477353,0.452741,0.399222,0.00415823,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.20075,0.314429,0.181415,0.282286,0.194707,0.616388,0.408413,0.516511,0.322213,0.28903,0.33942,0.0700181,0.0871388,0.522605,0.802166,0.537348,0.0267088,0.102227,0.416292,0.462712,0.382478,0.579431,0.204817,0.452428,0.138871,0.027191,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.178743,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.119167,0.351067,0.275347,0.637444,0.305885,0.241132,0.000122364,0.30666,0.303709,0.495883,0.386538,0.159081,0.250964,1.17227e-05,0.457886,0.0344603,0.220231,0.509064,0.020816,0.191517,0.0254647,0.235208,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.00107377,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.0267847,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.0218443,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.0262794,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.0246892,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.0025753,0.00132285,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.00452173,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.0251447,0.252796,0.205954,0.0750181
}}
}}

Revision as of 19:53, 8 August 2012


Full id: C4288_Fibroblast_amniotic_Smooth_Synoviocyte_salivary_gastric_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr3:14166542..14166566,+p3@TMEM43
Hg19::chr3:14166567..14166598,+p2@TMEM43
Hg19::chr3:14166625..14166649,+p1@TMEM43


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 cell1.19e-21180
fibroblast9.75e-1975
somatic cell2.68e-13591
animal cell1.24e-12679
eukaryotic cell1.24e-12679
skin fibroblast3.63e-1023
mesodermal cell4.66e-09119
embryonic cell2.78e-08248
fat cell7.66e-0815
contractile cell2.32e-0759
muscle precursor cell3.28e-0757
myoblast3.28e-0757
multi-potent skeletal muscle stem cell3.28e-0757
muscle cell6.89e-0754
Uber Anatomy
Ontology termp-valuen
surface structure1.90e-1395
mesoderm7.74e-12448
mesoderm-derived structure7.74e-12448
presumptive mesoderm7.74e-12448
multi-cellular organism8.20e-11659
integument9.78e-1045
integumental system9.78e-1045
splanchnic layer of lateral plate mesoderm1.59e-0984
somite2.93e-0983
paraxial mesoderm2.93e-0983
presomitic mesoderm2.93e-0983
presumptive segmental plate2.93e-0983
trunk paraxial mesoderm2.93e-0983
presumptive paraxial mesoderm2.93e-0983
multilaminar epithelium6.61e-0982
skin of body7.06e-0940
anatomical system2.21e-08625
trunk2.57e-08216
anatomical group3.82e-08626
dermomyotome5.06e-0870
organ component layer7.36e-0857
vasculature1.08e-0779
vascular system1.08e-0779
skeletal muscle tissue2.76e-0761
striated muscle tissue2.76e-0761
myotome2.76e-0761
muscle tissue3.42e-0763
musculature3.42e-0763
musculature of body3.42e-0763
trunk mesenchyme4.29e-07143
artery4.74e-0742
arterial blood vessel4.74e-0742
arterial system4.74e-0742
blood vessel5.92e-0760
epithelial tube open at both ends5.92e-0760
blood vasculature5.92e-0760
vascular cord5.92e-0760
vessel6.56e-0769
extraembryonic membrane8.52e-0714
membranous layer8.52e-0714


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4288&oldid=1993193"