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Coexpression cluster:C4648: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.17e-14!115;UBERON:0000914!1.37e-13!83;UBERON:0002329!1.37e-13!83;UBERON:0003077!1.37e-13!83;UBERON:0003059!1.37e-13!83;UBERON:0007282!1.37e-13!83;UBERON:0009618!1.37e-13!83;UBERON:0007285!1.37e-13!83;UBERON:0004290!2.96e-12!70;UBERON:0000468!7.93e-11!659;UBERON:0002204!1.33e-10!167;UBERON:0002385!2.91e-10!63;UBERON:0001015!2.91e-10!63;UBERON:0000383!2.91e-10!63;UBERON:0000480!6.21e-10!626;UBERON:0000467!6.51e-10!625;UBERON:0000486!1.18e-09!82;UBERON:0001134!2.18e-09!61;UBERON:0002036!2.18e-09!61;UBERON:0003082!2.18e-09!61;UBERON:0000479!2.64e-09!787;UBERON:0000062!5.26e-08!511;UBERON:0005256!3.48e-07!143;UBERON:0003102!4.30e-07!95;UBERON:0000926!9.91e-07!448;UBERON:0004120!9.91e-07!448;UBERON:0006603!9.91e-07!448
|ontology_enrichment_uberon=UBERON:0007023!2.17e-14!115;UBERON:0000914!1.37e-13!83;UBERON:0002329!1.37e-13!83;UBERON:0003077!1.37e-13!83;UBERON:0003059!1.37e-13!83;UBERON:0007282!1.37e-13!83;UBERON:0009618!1.37e-13!83;UBERON:0007285!1.37e-13!83;UBERON:0004290!2.96e-12!70;UBERON:0000468!7.93e-11!659;UBERON:0002204!1.33e-10!167;UBERON:0002385!2.91e-10!63;UBERON:0001015!2.91e-10!63;UBERON:0000383!2.91e-10!63;UBERON:0000480!6.21e-10!626;UBERON:0000467!6.51e-10!625;UBERON:0000486!1.18e-09!82;UBERON:0001134!2.18e-09!61;UBERON:0002036!2.18e-09!61;UBERON:0003082!2.18e-09!61;UBERON:0000479!2.64e-09!787;UBERON:0000062!5.26e-08!511;UBERON:0005256!3.48e-07!143;UBERON:0003102!4.30e-07!95;UBERON:0000926!9.91e-07!448;UBERON:0004120!9.91e-07!448;UBERON:0006603!9.91e-07!448
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191092306933505!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032420468462872!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168404903534005!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393428839009904!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109167420606593!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00668322919308626!REST#5978;3:9.65002871612802:0.00111263624711459:0.00771034549879906!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278211740659945!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191125760174184
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.0460856,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.0108656,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,5.20686e-05,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.000731968,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.00295997,0.054569,0.0504887,0.0709764,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.00472557,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.000133364,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.0128549,0.596561,0.0693171,0.00505227,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,5.10052e-08,0.00679439,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0014925,0.0799324,0.090079,0.140334,0.0176328,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.0187509,0.122935,0.228812,0.00660014,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.0128655,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.00500828,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.782949,0.635872,0.20128,0.823736,0.228731,0.335423,0.629514,0.261553,0.446302,0.373681,0.053682,0.147559,0.330703,0.395854,0.329568,0.53472,0.615744,0.271958,0.0475727,0.405773,0.0921263,0.217139,0.230901,0.187251,0.362792,0.181715,0.423979,0.00628346,0.0620388,0.218329,0.107929,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.236436,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.241757,0.18237,0.706298,0.513427,0.747852,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.0367769,0.522083,0.248634,0.0439966,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.581837,0.1002,0.305671,0.546839,0.551561,0.448039,0.218623,0.312808,0.695172,0.0451077,0.00286634,0.229003,0.650179,0.589326,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.319027,1.25716e-06,0.807485,0.428671,0.228096,0.336314,0.19763,0.000720848,0.567452,0.421464,0.48267,0.104399,0.165111,0.135248,0.335105,0.144809,0.145539,0.0134194,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.169823,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.130283,0.753577,0.206222,0.525396,0.651524,0.437176,0.040018,0.339277,0.192529,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.11631,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.00605613,0.279795,0.390395,0.0464827,0.0152726,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0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}}
}}

Revision as of 14:17, 5 September 2012


Full id: C4648_chronic_smooth_mature_aorta_bladder_heart_mesenchymal



Phase1 CAGE Peaks

Hg19::chr7:120628737..120628818,+p1@C7orf58
Hg19::chr7:120628828..120628878,+p2@C7orf58
Hg19::chr7:120628882..120628908,+p6@C7orf58


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 cell5.97e-14180
fibroblast8.24e-1275
skin fibroblast5.82e-1023
muscle precursor cell3.02e-0857
myoblast3.02e-0857
multi-potent skeletal muscle stem cell3.02e-0857
muscle cell2.27e-0754
Uber Anatomy
Ontology termp-valuen
adult organism2.17e-14115
somite1.37e-1383
paraxial mesoderm1.37e-1383
presomitic mesoderm1.37e-1383
presumptive segmental plate1.37e-1383
trunk paraxial mesoderm1.37e-1383
presumptive paraxial mesoderm1.37e-1383
dermomyotome2.96e-1270
multi-cellular organism7.93e-11659
musculoskeletal system1.33e-10167
muscle tissue2.91e-1063
musculature2.91e-1063
musculature of body2.91e-1063
anatomical group6.21e-10626
anatomical system6.51e-10625
multilaminar epithelium1.18e-0982
skeletal muscle tissue2.18e-0961
striated muscle tissue2.18e-0961
myotome2.18e-0961
tissue2.64e-09787
organ5.26e-08511
trunk mesenchyme3.48e-07143
surface structure4.30e-0795
mesoderm9.91e-07448
mesoderm-derived structure9.91e-07448
presumptive mesoderm9.91e-07448


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
CCNT2#90536.336201576962630.003930750035764890.0191092306933505
E2F6#187635.017155731697390.00791769806886330.032420468462872
EP300#203336.77394172622320.003216880500103790.0168404903534005
HDAC2#3066313.41562023662630.0004140761399857210.00393428839009904
HMGN3#932438.178547723350590.001827766942164210.0109167420606593
RAD21#5885310.35503389545630.0009004912073565420.00668322919308626
REST#597839.650028716128020.001112636247114590.00771034549879906
SIN3A#2594235.408884726815140.006318961977991520.0278211740659945
USF1#739136.361499277207960.00388404057290560.0191125760174184



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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