Personal tools

Coexpression cluster:C1219

From FANTOM5_SSTAR

Revision as of 14:45, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1219_Smooth_Tracheal_penis_tongue_skeletal_leiomyoma_diaphragm



Phase1 CAGE Peaks

Hg19::chr16:30078811..30078840,+p12@ALDOA
Hg19::chr16:30078876..30078906,+p9@ALDOA
Hg19::chr16:30079963..30079982,+p17@ALDOA
Hg19::chr16:30080136..30080158,+p15@ALDOA
Hg19::chr16:30080170..30080194,+p16@ALDOA
Hg19::chr16:30080217..30080237,+p14@ALDOA
Hg19::chr16:30080645..30080685,+p@chr16:30080645..30080685
+


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
epithelial vesicle8.98e-1678
dense mesenchyme tissue1.46e-1473
paraxial mesoderm2.30e-1472
presumptive paraxial mesoderm2.30e-1472
somite3.42e-1471
presomitic mesoderm3.42e-1471
presumptive segmental plate3.42e-1471
dermomyotome3.42e-1471
trunk paraxial mesoderm3.42e-1471
artery8.81e-1442
arterial blood vessel8.81e-1442
arterial system8.81e-1442
mesoderm2.54e-13315
mesoderm-derived structure2.54e-13315
presumptive mesoderm2.54e-13315
skeletal muscle tissue1.34e-1262
striated muscle tissue1.34e-1262
myotome1.34e-1262
multilaminar epithelium2.43e-1283
muscle tissue5.15e-1264
musculature5.15e-1264
musculature of body5.15e-1264
epithelial tube open at both ends7.48e-1159
blood vessel7.48e-1159
blood vasculature7.48e-1159
vascular cord7.48e-1159
systemic artery3.38e-1033
systemic arterial system3.38e-1033
splanchnic layer of lateral plate mesoderm3.94e-1083
musculoskeletal system1.02e-09167
vessel1.26e-0968
vasculature9.50e-0978
vascular system9.50e-0978
lateral plate mesoderm3.44e-08203
trunk mesenchyme4.51e-08122
circulatory system1.33e-07112
cardiovascular system5.26e-07109
epithelial tube8.23e-07117


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
CTCF#1066464.594505462635740.0002478392075687640.00267508050839956
POLR2A#543072.147453176558070.004747636447610280.022342108004865
RAD21#588545.917162225975040.002393184937227960.01355432980798
SMC3#912648.597104482818770.0005798466280161370.00486727230215217



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.