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Coexpression cluster:C1896: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,1.57264,0.733342,0.866061,0.859849,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.167776,0.500405,0.770467,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,1.00769,0.301779,1.06799,0.580638,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,1.17039,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.675933,0.917983,0.987729,0.543014,0.796279,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,2.46073,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
}}
}}

Revision as of 15:10, 26 November 2012


Full id: C1896_Smooth_mesenchymal_heart_tongue_left_Fibroblast_Endothelial



Phase1 CAGE Peaks

Hg19::chr2:228743006..228743014,+p@chr2:228743006..228743014
+
Hg19::chr3:112081052..112081065,-p@chr3:112081052..112081065
-
Hg19::chr3:112081099..112081112,-p@chr3:112081099..112081112
-
Hg19::chr5:63961948..63961959,-p@chr5:63961948..63961959
-
Hg19::chr8:96701429..96701463,-p@chr8:96701429..96701463
-


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
heart blood vessel4.63e-535
coronary vessel4.63e-535
coronary artery3.13e-503
systemic artery5.61e-4033
systemic arterial system5.61e-4033
artery1.27e-3842
arterial blood vessel1.27e-3842
arterial system1.27e-3842
brachiocephalic artery5.07e-342
brachiocephalic vasculature5.07e-342
thoracic segment blood vessel1.16e-305
subclavian artery1.16e-305
splanchnic layer of lateral plate mesoderm8.85e-2883
epithelial tube open at both ends2.52e-2759
blood vessel2.52e-2759
blood vasculature2.52e-2759
vascular cord2.52e-2759
heart1.87e-2424
primitive heart tube1.87e-2424
primary heart field1.87e-2424
anterior lateral plate mesoderm1.87e-2424
heart tube1.87e-2424
heart primordium1.87e-2424
cardiac mesoderm1.87e-2424
cardiogenic plate1.87e-2424
heart rudiment1.87e-2424
vessel1.27e-2368
trunk blood vessel3.98e-227
primary circulatory organ9.84e-2227
cardiovascular system5.64e-21109
vasculature1.66e-2078
vascular system1.66e-2078
circulatory system2.16e-20112
epithelial tube1.73e-19117
skeletal muscle tissue1.22e-1662
striated muscle tissue1.22e-1662
myotome1.22e-1662
muscle tissue4.19e-1664
musculature4.19e-1664
musculature of body4.19e-1664
somite1.82e-1471
presomitic mesoderm1.82e-1471
presumptive segmental plate1.82e-1471
dermomyotome1.82e-1471
trunk paraxial mesoderm1.82e-1471
paraxial mesoderm2.95e-1472
presumptive paraxial mesoderm2.95e-1472
dense mesenchyme tissue4.70e-1473
epithelial vesicle4.06e-1378
multilaminar epithelium2.71e-1283
tube1.81e-11192
lateral plate mesoderm8.49e-11203
internal thoracic artery1.03e-092
mixed ectoderm/mesoderm/endoderm-derived structure1.44e-092
developing epithelial placode1.44e-092
respiratory system arterial blood vessel1.44e-092
respiratory system blood vessel1.44e-092
respiratory system artery1.44e-092
head blood vessel1.44e-092
pulmonary artery1.44e-092
pulmonary vascular system1.44e-092
pharyngeal vasculature1.44e-092
truncus arteriosus1.44e-092
aortic sac1.44e-092
pharyngeal arch artery1.44e-092
anatomical conduit5.49e-09240
compound organ1.57e-0868
unilaminar epithelium2.15e-08148
trunk mesenchyme3.62e-08122
epithelium7.99e-07306
outflow tract8.62e-073
cell layer9.54e-07309


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)

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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.