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Coexpression cluster:C4137: Difference between revisions

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|full_id=C4137_Smooth_Fibroblast_Chondrocyte_Mesenchymal_Preadipocyte_mesenchymal_Ewing
|full_id=C4137_Smooth_Fibroblast_Chondrocyte_Mesenchymal_Preadipocyte_mesenchymal_Ewing
|id=C4137
|id=C4137
|ontology_enrichment_celltype=CL:0000055!1.68e-41!180;CL:0000680!2.53e-22!57;CL:0000056!2.53e-22!57;CL:0000355!2.53e-22!57;CL:0000187!1.57e-20!54;CL:0000057!4.06e-19!75;CL:0000183!1.63e-18!59;CL:0000393!7.21e-17!60;CL:0000211!7.21e-17!60;CL:0000192!8.54e-17!42;CL:0000514!8.54e-17!42;CL:0000359!1.39e-13!32;CL:0000222!4.21e-09!119;CL:0002620!2.40e-08!23;CL:0002334!8.64e-08!12;CL:0002494!1.53e-07!16
|ontology_enrichment_celltype=CL:0000680!1.01e-24!58;CL:0000056!1.01e-24!58;CL:0000355!1.01e-24!58;CL:0000187!1.26e-22!55;CL:0000055!2.20e-20!106;CL:0000183!2.70e-20!59;CL:0000192!1.00e-19!43;CL:0000514!1.00e-19!43;CL:0000393!7.30e-19!61;CL:0000211!7.30e-19!61;CL:0000057!2.14e-18!76;CL:0000359!1.75e-16!32;CL:0002371!1.35e-11!588;CL:0000222!2.06e-11!121;CL:0000048!3.88e-11!427;CL:0000723!1.66e-10!433;CL:0000034!2.40e-09!441;CL:0002334!2.61e-08!12;CL:0002494!1.18e-07!16;CL:0002539!4.46e-07!10;CL:0002321!5.80e-07!250;CL:0002620!6.57e-07!23;CL:0000548!9.86e-07!679;CL:0000255!9.86e-07!679
|ontology_enrichment_disease=DOID:2394!6.15e-09!14
|ontology_enrichment_disease=DOID:2394!1.74e-10!14
|ontology_enrichment_uberon=UBERON:0000914!2.47e-26!83;UBERON:0002329!2.47e-26!83;UBERON:0003077!2.47e-26!83;UBERON:0003059!2.47e-26!83;UBERON:0007282!2.47e-26!83;UBERON:0009618!2.47e-26!83;UBERON:0007285!2.47e-26!83;UBERON:0004290!1.99e-23!70;UBERON:0001134!3.37e-22!61;UBERON:0002036!3.37e-22!61;UBERON:0003082!3.37e-22!61;UBERON:0000486!8.34e-22!82;UBERON:0002385!9.97e-22!63;UBERON:0001015!9.97e-22!63;UBERON:0000383!9.97e-22!63;UBERON:0000475!6.86e-15!365;UBERON:0005256!2.18e-14!143;UBERON:0003102!4.00e-12!95;UBERON:0004872!2.35e-11!84;UBERON:0000481!2.91e-11!347;UBERON:0001637!3.49e-10!42;UBERON:0003509!3.49e-10!42;UBERON:0004572!3.49e-10!42;UBERON:0000468!1.28e-09!659;UBERON:0004573!1.55e-09!33;UBERON:0004571!1.55e-09!33;UBERON:0002199!1.81e-09!45;UBERON:0002416!1.81e-09!45;UBERON:0000119!5.01e-09!312;UBERON:0002049!1.21e-08!79;UBERON:0007798!1.21e-08!79;UBERON:0000483!1.46e-08!309;UBERON:0002097!2.46e-08!40;UBERON:0002100!2.56e-08!216;UBERON:0000948!5.39e-08!24;UBERON:0005498!5.39e-08!24;UBERON:0004140!5.39e-08!24;UBERON:0009881!5.39e-08!24;UBERON:0004141!5.39e-08!24;UBERON:0003084!5.39e-08!24;UBERON:0007005!5.39e-08!24;UBERON:0004139!5.39e-08!24;UBERON:0004291!5.39e-08!24;UBERON:0000490!8.36e-08!138;UBERON:0007100!1.41e-07!27;UBERON:0001009!1.76e-07!113;UBERON:0004535!1.77e-07!110;UBERON:0001981!2.78e-07!60;UBERON:0007500!2.78e-07!60;UBERON:0004537!2.78e-07!60;UBERON:0006965!2.78e-07!60;UBERON:0003104!2.86e-07!238;UBERON:0009142!2.86e-07!238;UBERON:0001135!4.18e-07!15;UBERON:0000467!6.43e-07!625;UBERON:0000480!9.25e-07!626
|ontology_enrichment_uberon=UBERON:0002329!1.34e-21!71;UBERON:0003059!1.34e-21!71;UBERON:0007282!1.34e-21!71;UBERON:0004290!1.34e-21!71;UBERON:0009618!1.34e-21!71;UBERON:0001134!1.42e-21!62;UBERON:0002036!1.42e-21!62;UBERON:0003082!1.42e-21!62;UBERON:0007524!4.12e-21!73;UBERON:0003077!6.01e-21!72;UBERON:0007285!6.01e-21!72;UBERON:0002385!3.61e-20!64;UBERON:0001015!3.61e-20!64;UBERON:0000383!3.61e-20!64;UBERON:0000486!3.11e-19!83;UBERON:0007503!1.41e-18!78;UBERON:0005256!1.78e-13!122;UBERON:0001637!1.85e-11!42;UBERON:0003509!1.85e-11!42;UBERON:0004572!1.85e-11!42;UBERON:0003104!2.33e-11!160;UBERON:0009142!2.33e-11!160;UBERON:0004872!1.08e-10!83;UBERON:0004573!3.21e-10!33;UBERON:0004571!3.21e-10!33;UBERON:0003102!3.66e-10!99;UBERON:0000475!1.90e-09!264;UBERON:0000490!6.63e-09!148;UBERON:0001009!1.52e-08!112;UBERON:0002049!1.79e-08!78;UBERON:0007798!1.79e-08!78;UBERON:0004535!2.58e-08!109;UBERON:0002199!5.91e-08!46;UBERON:0002416!5.91e-08!46;UBERON:0000926!6.37e-08!315;UBERON:0004120!6.37e-08!315;UBERON:0006603!6.37e-08!315;UBERON:0007100!2.59e-07!27;UBERON:0000948!2.95e-07!24;UBERON:0005498!2.95e-07!24;UBERON:0004140!2.95e-07!24;UBERON:0009881!2.95e-07!24;UBERON:0004141!2.95e-07!24;UBERON:0003084!2.95e-07!24;UBERON:0007005!2.95e-07!24;UBERON:0004139!2.95e-07!24;UBERON:0004291!2.95e-07!24;UBERON:0001135!3.13e-07!15;UBERON:0004237!4.46e-07!10;UBERON:0004695!4.46e-07!10;UBERON:0002111!4.46e-07!10;UBERON:0004178!4.46e-07!10;UBERON:0002097!4.66e-07!41;UBERON:0007500!6.57e-07!59;UBERON:0001981!6.57e-07!59;UBERON:0004537!6.57e-07!59;UBERON:0006965!6.57e-07!59;UBERON:0002100!8.00e-07!199
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167757418759844!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00643643426255324
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167757418759844!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00643643426255324
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220026,0.00594521,0.0043762,0.00481323,0.173708,0.0104618,0.211595,0.0300692,0.000420877,0.0445237,0.052362,0.00179985,0.153187,0.0797897,0.00016623,0.0135691,0.123526,0.000133184,0.0558058,0.28262,0.0377931,0.137332,0.0145999,4.97064e-05,0.00188014,0.0021409,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.000234172,0.11002,0.26144,3.98541e-06,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.000242011,0.217069,0.190048,0.131088,0.394069,0.0027004,0.286988,0.0761239,0.0158143,0.0818785,0.182701,0.0637246,0.011488,0.141463,0.0148418,0.140622,0.0889592,0.309588,0.28711,1.72531e-11,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.00292564,0.0936516,0.144075,0.0340203,0.00282206,0.277091,0.739716,0.0232393,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.0271723,0.0472142,0.0355833,0.125606,0.175094,0.911304,0.936279,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.00171529,0.00293103,0.045654,0.00631005,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.00446076,0.172425,0.104948,0.221645,0.057168,0.00259914,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.00136247,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.0126914,0.170295,0.193653,0.137219,0.0282663,0.251466,0.288096,0.11903,0.0838874,0.000795326,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.00352872,0.103667,0.000263206,0.000329372,0.16791,0.09066,0.0597157,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0161946,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.120614,0.407369,0.231447,0.544776,0.43956,5.96881e-07,0.0189483,0.448797,0.197484,0.0148336,0.00010434,0.406019,0.381071,0.580441,0.643768,0.432035,0.722159,0.390366,0.48809,0.50058,0.443185,0.169835,0.875915,0.871256,0.227104,0.518585,0.617852,0.38649,0.284625,0.504757,0.55194,0.729153,0.0465139,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.00293755,0.777351,0.0889613,0.73485,0.683217,0.161598,0.751174,0.644754,0.496032,0.799185,0.37357,0.78509,0.477353,0.78384,0.746954,0.771991,0.20342,0.200493,0.20558,0.0505073,0.25656,0.425963,0.349197,0.383291,0.000717871,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.0175523,0.282286,0.78,0.616388,0.01635,0.165147,0.322213,0.656109,0.33942,0.61031,0.387276,0.169614,0.802166,0.537348,0.222037,0.0175112,0.0174635,0.128937,0.734551,0.579431,0.204817,0.000401229,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,1.88237e-06,0.332919,0.373557,0.523625,0.408861,0.0111982,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.119167,0.351067,0.275347,0.637444,0.305885,0.00285094,0.371414,0.0527347,0.303709,0.495883,0.386538,0.508064,9.33057e-10,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.0254647,0.601877,0.307334,0.459728,6.78075e-08,0.563586,0.472935,0.0151656,0.0413011,0.368095,0.0418805,0.00157463,0.47795,0.0105648,4.98512e-06,0.197805,0.608187,0.0870376,0.332774,0.52832,0.00579439,0.0814305,0.00170684,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.0192444,0.258854,0.188263,0.0719199,9.06634e-07,0.162568,0.19104,0.0140817,0.219428,0.208013,0.0900729,0.000155666,3.92648e-05,0.252184,0.0828367,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.222977,0.341681,0.0542164,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,1.15352e-05,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.000103317,0.00394192,0.000263373,0.145701,0.229428,0.0139199,0.0284767,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,3.68621e-05,0.0251995,0.158479,0.220319,0.195218,0.124213,0.0370716,0.30793,0.180606,0.159884,0.257294,0.150733,5.97373e-06,0.00801612,0.00121059,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.00176424,0.141867,0.193031,0.00316602,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.00072309,0.13108,0.256963,0.00221189,0.172134,0.0166394,0.00485777,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,8.4053e-05,0.0407233,0.0537355,0.00717361,0.261724,0.211332,0.187731,0.0297055,0.189559,0.0812887,0.0981146,0.064145,0.000332324,0.0638699,0.104603,0.00224987,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.000455851,9.49159e-05,3.30228e-05,0.0457063,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.00482769,0.264413,0.131761,0.16065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}}
}}

Revision as of 15:42, 19 October 2012


Full id: C4137_Smooth_Fibroblast_Chondrocyte_Mesenchymal_Preadipocyte_mesenchymal_Ewing



Phase1 CAGE Peaks

Hg19::chr2:163099885..163099963,-p1@FAP
Hg19::chr2:163099985..163099996,-p3@FAP
Hg19::chr2:163100045..163100071,-p2@FAP


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
somite1.34e-2171
presomitic mesoderm1.34e-2171
presumptive segmental plate1.34e-2171
dermomyotome1.34e-2171
trunk paraxial mesoderm1.34e-2171
skeletal muscle tissue1.42e-2162
striated muscle tissue1.42e-2162
myotome1.42e-2162
dense mesenchyme tissue4.12e-2173
paraxial mesoderm6.01e-2172
presumptive paraxial mesoderm6.01e-2172
muscle tissue3.61e-2064
musculature3.61e-2064
musculature of body3.61e-2064
multilaminar epithelium3.11e-1983
epithelial vesicle1.41e-1878
trunk mesenchyme1.78e-13122
artery1.85e-1142
arterial blood vessel1.85e-1142
arterial system1.85e-1142
mesenchyme2.33e-11160
entire embryonic mesenchyme2.33e-11160
splanchnic layer of lateral plate mesoderm1.08e-1083
systemic artery3.21e-1033
systemic arterial system3.21e-1033
surface structure3.66e-1099
organism subdivision1.90e-09264
unilaminar epithelium6.63e-09148
circulatory system1.52e-08112
vasculature1.79e-0878
vascular system1.79e-0878
cardiovascular system2.58e-08109
integument5.91e-0846
integumental system5.91e-0846
mesoderm6.37e-08315
mesoderm-derived structure6.37e-08315
presumptive mesoderm6.37e-08315
primary circulatory organ2.59e-0727
heart2.95e-0724
primitive heart tube2.95e-0724
primary heart field2.95e-0724
anterior lateral plate mesoderm2.95e-0724
heart tube2.95e-0724
heart primordium2.95e-0724
cardiac mesoderm2.95e-0724
cardiogenic plate2.95e-0724
heart rudiment2.95e-0724
smooth muscle tissue3.13e-0715
blood vessel smooth muscle4.46e-0710
arterial system smooth muscle4.46e-0710
artery smooth muscle tissue4.46e-0710
aorta smooth muscle tissue4.46e-0710
skin of body4.66e-0741
epithelial tube open at both ends6.57e-0759
blood vessel6.57e-0759
blood vasculature6.57e-0759
vascular cord6.57e-0759
trunk8.00e-07199
Disease
Ontology termp-valuen
ovarian cancer1.74e-1014


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
EP300#203336.77394172622320.003216880500103790.0167757418759844
STAT3#6774310.51946499715420.0008589184530415310.00643643426255324



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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