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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1133_mature_smooth_bladder_aorta_heart_adipose_penis
|full_id=C1133_mature_smooth_bladder_aorta_heart_adipose_penis
|id=C1133
|id=C1133

Revision as of 13:36, 12 September 2012


Full id: C1133_mature_smooth_bladder_aorta_heart_adipose_penis



Phase1 CAGE Peaks

Hg19::chr11:119188110..119188132,-p4@MCAM
Hg19::chr16:55867146..55867153,-p3@CES1
Hg19::chr17:41004597..41004617,+p@chr17:41004597..41004617
+
Hg19::chr2:218785644..218785662,-p@chr2:218785644..218785662
-
Hg19::chr2:218808771..218808802,-p1@TNS1
Hg19::chr8:30241649..30241675,+p6@RBPMS
Hg19::chr8:30241679..30241690,+p12@RBPMS


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>

Cell Type
Ontology termp-valuen
fat cell8.73e-0815
Uber Anatomy
Ontology termp-valuen
adult organism3.07e-36115
tube5.74e-23194
anatomical conduit7.84e-22241
multi-cellular organism1.09e-20659
anatomical cluster7.99e-18286
anatomical system9.54e-18625
anatomical group2.02e-17626
organism subdivision7.51e-14365
epithelial tube1.82e-13118
neural tube3.17e-1357
neural rod3.17e-1357
future spinal cord3.17e-1357
neural keel3.17e-1357
epithelium8.98e-13309
cell layer1.88e-12312
regional part of brain7.99e-1259
embryo3.74e-11612
neural plate1.21e-1086
presumptive neural plate1.21e-1086
embryonic structure1.37e-10605
developing anatomical structure1.37e-10605
anterior neural tube1.63e-1042
germ layer2.80e-10604
embryonic tissue2.80e-10604
presumptive structure2.80e-10604
epiblast (generic)2.80e-10604
regional part of forebrain5.63e-1041
forebrain5.63e-1041
future forebrain5.63e-1041
multi-tissue structure6.71e-10347
central nervous system7.79e-1082
organ9.11e-10511
splanchnic layer of lateral plate mesoderm1.44e-0984
neurectoderm2.86e-0990
brain3.78e-0969
future brain3.78e-0969
regional part of nervous system4.59e-0994
nervous system4.59e-0994
vessel9.94e-0969
blood vessel1.75e-0860
epithelial tube open at both ends1.75e-0860
blood vasculature1.75e-0860
vascular cord1.75e-0860
gray matter1.84e-0834
brain grey matter1.84e-0834
vasculature1.96e-0879
vascular system1.96e-0879
telencephalon1.97e-0834
regional part of telencephalon3.88e-0833
compound organ7.86e-0869
cerebral hemisphere1.45e-0732
abdominal segment of trunk2.46e-0761
abdomen2.46e-0761
circulatory system3.93e-07113
trunk mesenchyme4.05e-07143
muscle tissue5.60e-0763
musculature5.60e-0763
musculature of body5.60e-0763
pre-chordal neural plate7.90e-0761
unilaminar epithelium9.86e-07138


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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