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Coexpression cluster:C1219: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1219_Smooth_Tracheal_penis_tongue_skeletal_leiomyoma_diaphragm
|full_id=C1219_Smooth_Tracheal_penis_tongue_skeletal_leiomyoma_diaphragm
|id=C1219
|id=C1219

Revision as of 13:43, 12 September 2012


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
dermomyotome6.83e-1570
artery5.96e-1442
arterial blood vessel5.96e-1442
arterial system5.96e-1442
multilaminar epithelium2.38e-1382
somite3.35e-1383
paraxial mesoderm3.35e-1383
presomitic mesoderm3.35e-1383
presumptive segmental plate3.35e-1383
trunk paraxial mesoderm3.35e-1383
presumptive paraxial mesoderm3.35e-1383
skeletal muscle tissue4.04e-1361
striated muscle tissue4.04e-1361
myotome4.04e-1361
muscle tissue1.78e-1263
musculature1.78e-1263
musculature of body1.78e-1263
blood vessel4.56e-1160
epithelial tube open at both ends4.56e-1160
blood vasculature4.56e-1160
vascular cord4.56e-1160
splanchnic layer of lateral plate mesoderm7.12e-1184
systemic artery3.05e-1033
systemic arterial system3.05e-1033
musculoskeletal system4.59e-10167
vessel4.93e-1069
vasculature3.06e-0979
vascular system3.06e-0979
lateral plate mesoderm1.67e-08216
circulatory system3.44e-08113
trunk mesenchyme9.09e-08143
mesoderm1.04e-07448
mesoderm-derived structure1.04e-07448
presumptive mesoderm1.04e-07448
epithelial tube1.53e-07118
cardiovascular system1.66e-07110


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.