Personal tools

Coexpression cluster:C471

From FANTOM5_SSTAR

Revision as of 14:14, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C471_Smooth_Fibroblast_leiomyoma_mesenchymal_Mesothelial_meningioma_Prostate



Phase1 CAGE Peaks

Hg19::chr8:42033234..42033247,-p@chr8:42033234..42033247
-
Hg19::chr8:42033253..42033264,-p@chr8:42033253..42033264
-
Hg19::chr8:42033364..42033376,-p@chr8:42033364..42033376
-
Hg19::chr8:42033383..42033398,-p@chr8:42033383..42033398
-
Hg19::chr8:42033546..42033576,-p@chr8:42033546..42033576
-
Hg19::chr8:42033578..42033605,-p@chr8:42033578..42033605
-
Hg19::chr8:42033607..42033639,-p@chr8:42033607..42033639
-
Hg19::chr8:42033640..42033671,-p@chr8:42033640..42033671
-
Hg19::chr8:42036444..42036460,+p@chr8:42036444..42036460
+
Hg19::chr8:42036539..42036561,-p@chr8:42036539..42036561
-
Hg19::chr8:42037500..42037536,-p@chr8:42037500..42037536
-
Hg19::chr8:42037883..42037900,-p@chr8:42037883..42037900
-
Hg19::chr8:42038055..42038068,-p3@PLAT
Hg19::chr8:42040287..42040298,-p10@PLAT
Hg19::chr8:42042635..42042650,-p4@PLAT
Hg19::chr8:42042654..42042665,-p9@PLAT
Hg19::chr8:42044953..42044969,-p@chr8:42044953..42044969
-
Hg19::chr8:42044977..42044996,-p@chr8:42044977..42044996
-
Hg19::chr8:42045498..42045512,-p6@PLAT
Hg19::chr8:42065075..42065090,-p1@PLAT
Hg19::chr8:42065187..42065201,-p2@PLAT


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
epithelial vesicle2.04e-2278
skeletal muscle tissue2.67e-2262
striated muscle tissue2.67e-2262
myotome2.67e-2262
muscle tissue3.24e-2264
musculature3.24e-2264
musculature of body3.24e-2264
systemic artery3.51e-2133
systemic arterial system3.51e-2133
somite1.04e-2071
presomitic mesoderm1.04e-2071
presumptive segmental plate1.04e-2071
dermomyotome1.04e-2071
trunk paraxial mesoderm1.04e-2071
artery1.90e-2042
arterial blood vessel1.90e-2042
arterial system1.90e-2042
paraxial mesoderm3.25e-2072
presumptive paraxial mesoderm3.25e-2072
dense mesenchyme tissue9.77e-2073
trunk mesenchyme2.15e-17122
multilaminar epithelium1.35e-1683
epithelial tube1.28e-15117
organism subdivision2.36e-15264
trunk7.74e-15199
smooth muscle tissue1.60e-1415
vasculature2.29e-1478
vascular system2.29e-1478
mesenchyme3.15e-14160
entire embryonic mesenchyme3.15e-14160
epithelial tube open at both ends1.71e-1359
blood vessel1.71e-1359
blood vasculature1.71e-1359
vascular cord1.71e-1359
unilaminar epithelium2.31e-13148
splanchnic layer of lateral plate mesoderm3.42e-1383
cell layer3.76e-13309
epithelium4.08e-13306
blood vessel smooth muscle3.08e-1210
arterial system smooth muscle3.08e-1210
artery smooth muscle tissue3.08e-1210
aorta smooth muscle tissue3.08e-1210
cardiovascular system7.71e-12109
multi-tissue structure1.63e-11342
vessel2.59e-1168
circulatory system3.75e-11112
aorta5.07e-1121
aortic system5.07e-1121
mesoderm4.04e-10315
mesoderm-derived structure4.04e-10315
presumptive mesoderm4.04e-10315
developing anatomical structure4.39e-08581
anatomical system1.12e-07624
embryo1.23e-07592
anatomical group1.33e-07625
anatomical cluster2.39e-07373
excretory tube3.70e-0716
kidney epithelium3.70e-0716
cortex of kidney3.89e-0712
renal parenchyma3.89e-0712
nephron tubule epithelium4.97e-0710
heart blood vessel5.95e-075
coronary vessel5.95e-075
anatomical conduit7.34e-07240
Disease
Ontology termp-valuen
ovarian cancer5.71e-0914


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
MEF2C#420835.901622070374860.01360717439201470.048017289036614



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.