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Coexpression cluster:C807: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000475!7.87e-20!264;UBERON:0002100!4.59e-17!199;UBERON:0003914!1.24e-15!117;UBERON:0000468!4.86e-15!656;UBERON:0003104!1.43e-14!160;UBERON:0009142!1.43e-14!160;UBERON:0000490!3.02e-14!148;UBERON:0002049!6.38e-14!78;UBERON:0007798!6.38e-14!78;UBERON:0001637!6.62e-14!42;UBERON:0003509!6.62e-14!42;UBERON:0004572!6.62e-14!42;UBERON:0005256!7.15e-14!122;UBERON:0000055!2.46e-13!68;UBERON:0007500!9.44e-13!59;UBERON:0001981!9.44e-13!59;UBERON:0004537!9.44e-13!59;UBERON:0006965!9.44e-13!59;UBERON:0000486!1.25e-12!83;UBERON:0000483!6.78e-12!306;UBERON:0004573!7.69e-12!33;UBERON:0004571!7.69e-12!33;UBERON:0000119!7.78e-12!309;UBERON:0007503!2.58e-11!78;UBERON:0003102!2.86e-11!99;UBERON:0007524!3.46e-11!73;UBERON:0002329!3.70e-11!71;UBERON:0003059!3.70e-11!71;UBERON:0007282!3.70e-11!71;UBERON:0004290!3.70e-11!71;UBERON:0009618!3.70e-11!71;UBERON:0003077!8.93e-11!72;UBERON:0007285!8.93e-11!72;UBERON:0004872!1.26e-10!83;UBERON:0000467!2.04e-10!624;UBERON:0000477!3.45e-10!373;UBERON:0000480!3.70e-10!625;UBERON:0001134!4.37e-10!62;UBERON:0002036!4.37e-10!62;UBERON:0003082!4.37e-10!62;UBERON:0002385!1.45e-09!64;UBERON:0001015!1.45e-09!64;UBERON:0000383!1.45e-09!64;UBERON:0000481!5.67e-09!342;UBERON:0004111!1.43e-08!240;UBERON:0004923!1.76e-08!66;UBERON:0000947!1.82e-07!21;UBERON:0010191!1.82e-07!21;UBERON:0004535!4.65e-07!109;UBERON:0002199!6.15e-07!46;UBERON:0002416!6.15e-07!46;UBERON:0004237!6.99e-07!10;UBERON:0004695!6.99e-07!10;UBERON:0002111!6.99e-07!10;UBERON:0004178!6.99e-07!10;UBERON:0001009!7.70e-07!112;UBERON:0002097!8.83e-07!41
|ontology_enrichment_uberon=UBERON:0000475!7.87e-20!264;UBERON:0002100!4.59e-17!199;UBERON:0003914!1.24e-15!117;UBERON:0000468!4.86e-15!656;UBERON:0003104!1.43e-14!160;UBERON:0009142!1.43e-14!160;UBERON:0000490!3.02e-14!148;UBERON:0002049!6.38e-14!78;UBERON:0007798!6.38e-14!78;UBERON:0001637!6.62e-14!42;UBERON:0003509!6.62e-14!42;UBERON:0004572!6.62e-14!42;UBERON:0005256!7.15e-14!122;UBERON:0000055!2.46e-13!68;UBERON:0007500!9.44e-13!59;UBERON:0001981!9.44e-13!59;UBERON:0004537!9.44e-13!59;UBERON:0006965!9.44e-13!59;UBERON:0000486!1.25e-12!83;UBERON:0000483!6.78e-12!306;UBERON:0004573!7.69e-12!33;UBERON:0004571!7.69e-12!33;UBERON:0000119!7.78e-12!309;UBERON:0007503!2.58e-11!78;UBERON:0003102!2.86e-11!99;UBERON:0007524!3.46e-11!73;UBERON:0002329!3.70e-11!71;UBERON:0003059!3.70e-11!71;UBERON:0007282!3.70e-11!71;UBERON:0004290!3.70e-11!71;UBERON:0009618!3.70e-11!71;UBERON:0003077!8.93e-11!72;UBERON:0007285!8.93e-11!72;UBERON:0004872!1.26e-10!83;UBERON:0000467!2.04e-10!624;UBERON:0000477!3.45e-10!373;UBERON:0000480!3.70e-10!625;UBERON:0001134!4.37e-10!62;UBERON:0002036!4.37e-10!62;UBERON:0003082!4.37e-10!62;UBERON:0002385!1.45e-09!64;UBERON:0001015!1.45e-09!64;UBERON:0000383!1.45e-09!64;UBERON:0000481!5.67e-09!342;UBERON:0004111!1.43e-08!240;UBERON:0004923!1.76e-08!66;UBERON:0000947!1.82e-07!21;UBERON:0010191!1.82e-07!21;UBERON:0004535!4.65e-07!109;UBERON:0002199!6.15e-07!46;UBERON:0002416!6.15e-07!46;UBERON:0004237!6.99e-07!10;UBERON:0004695!6.99e-07!10;UBERON:0002111!6.99e-07!10;UBERON:0004178!6.99e-07!10;UBERON:0001009!7.70e-07!112;UBERON:0002097!8.83e-07!41
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11364,0.00793133,0.189925
|tfbs_overrepresentation_for_novel_motifs=0.280498,0.0347211,0.273994,0.404877,0.237701,0.403356,0.474413,0.434224,0.138703,0.0921938,0.375531,0.515448,1.16754,0.46359,0.666154,0.256724,0.68716,0.191625,0.116269,0.178097,0.752779,0.111654,0.396189,0.233338,0.314616,0.537051,0.310025,0.39419,0.240354,0.281506,0.355553,0.722879,0.165252,0.108961,0.20845,0.200804,0.20579,0.404426,0.186493,0.125439,0.207288,0.903115,0.031261,0.235234,0.235672,0.301189,0.47544,0.365597,0.116302,0.240465,0.550604,0.486559,0.468946,0.797754,0.947672,0.466348,1.96373,0.435652,0.0825677,0.434711,0.762758,0.477672,0.848838,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.144996,0.0579262,0.945703,0.104203,0.0955465,0.0867529,0.644006,0.709631,0.309107,0.380738,0.659298,1.23725,1.39374,0.89511,0.0102458,0.70174,0.0795497,0.575506,1.4989,1.12715,0.868602,0.739223,0.509773,0.238337,1.02531,0.368981,0.780743,0.579925,0.524614,0.187593,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.637089,0.7752,0.772599,0.741574,0.384185,1.07963,0.204477,0.0136871,0.354459,0.624851,0.173291,0.937551,1.4047,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,1.02842,0.869279,0.358161,2.27323,0.50181,1.13991,0.260985,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.337738,0.971618,0.052013,0.0287097,0.869654,0.414185,1.2007,1.26919,0.560015,0.225815,0.314669,0.28899,1.05976,0.851493,0.708865,0.291837,0.633206,0.493542,0.931981,0.473159,0.02648
}}
}}

Revision as of 14:29, 26 November 2012


Full id: C807_neuroectodermal_renal_leiomyoma_Smooth_neuroblastoma_Aortic_Melanocyte



Phase1 CAGE Peaks

Hg19::chr11:69466307..69466329,+p@chr11:69466307..69466329
+
Hg19::chr11:69466430..69466446,+p@chr11:69466430..69466446
+
Hg19::chr11:69466577..69466634,+p@chr11:69466577..69466634
+
Hg19::chr11:69467214..69467238,+p5@CCND1
Hg19::chr11:69467344..69467411,+p2@CCND1
Hg19::chr11:69467416..69467438,+p7@CCND1
Hg19::chr11:69467457..69467532,+p3@CCND1
Hg19::chr11:69467977..69467992,+p@chr11:69467977..69467992
+
Hg19::chr11:69468195..69468212,+p@chr11:69468195..69468212
+
Hg19::chr11:69468466..69468480,+p@chr11:69468466..69468480
+


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
organism subdivision7.87e-20264
trunk4.59e-17199
epithelial tube1.24e-15117
multi-cellular organism4.86e-15656
mesenchyme1.43e-14160
entire embryonic mesenchyme1.43e-14160
unilaminar epithelium3.02e-14148
vasculature6.38e-1478
vascular system6.38e-1478
artery6.62e-1442
arterial blood vessel6.62e-1442
arterial system6.62e-1442
trunk mesenchyme7.15e-14122
vessel2.46e-1368
epithelial tube open at both ends9.44e-1359
blood vessel9.44e-1359
blood vasculature9.44e-1359
vascular cord9.44e-1359
multilaminar epithelium1.25e-1283
epithelium6.78e-12306
systemic artery7.69e-1233
systemic arterial system7.69e-1233
cell layer7.78e-12309
epithelial vesicle2.58e-1178
surface structure2.86e-1199
dense mesenchyme tissue3.46e-1173
somite3.70e-1171
presomitic mesoderm3.70e-1171
presumptive segmental plate3.70e-1171
dermomyotome3.70e-1171
trunk paraxial mesoderm3.70e-1171
paraxial mesoderm8.93e-1172
presumptive paraxial mesoderm8.93e-1172
splanchnic layer of lateral plate mesoderm1.26e-1083
anatomical system2.04e-10624
anatomical cluster3.45e-10373
anatomical group3.70e-10625
skeletal muscle tissue4.37e-1062
striated muscle tissue4.37e-1062
myotome4.37e-1062
muscle tissue1.45e-0964
musculature1.45e-0964
musculature of body1.45e-0964
multi-tissue structure5.67e-09342
anatomical conduit1.43e-08240
organ component layer1.76e-0866
aorta1.82e-0721
aortic system1.82e-0721
cardiovascular system4.65e-07109
integument6.15e-0746
integumental system6.15e-0746
blood vessel smooth muscle6.99e-0710
arterial system smooth muscle6.99e-0710
artery smooth muscle tissue6.99e-0710
aorta smooth muscle tissue6.99e-0710
circulatory system7.70e-07112
skin of body8.83e-0741
Disease
Ontology termp-valuen
cell type cancer6.17e-07143


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.

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