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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C635_Fibroblast_Pericytes_Nucleus_Preadipocyte_Smooth_mesothelioma_Prostate
|full_id=C635_Fibroblast_Pericytes_Nucleus_Preadipocyte_Smooth_mesothelioma_Prostate
|id=C635
|id=C635

Revision as of 18:17, 12 September 2012


Full id: C635_Fibroblast_Pericytes_Nucleus_Preadipocyte_Smooth_mesothelioma_Prostate



Phase1 CAGE Peaks

Hg19::chr3:170136642..170136663,+p1@CLDN11
Hg19::chr3:170140945..170141037,+p@chr3:170140945..170141037
+
Hg19::chr3:170150373..170150387,+p@chr3:170150373..170150387
+
Hg19::chr3:170150429..170150439,+p@chr3:170150429..170150439
+
Hg19::chr3:170150498..170150515,+p@chr3:170150498..170150515
+
Hg19::chr3:170150547..170150552,+p@chr3:170150547..170150552
+
Hg19::chr3:170150588..170150600,+p@chr3:170150588..170150600
+
Hg19::chr3:170150614..170150632,+p@chr3:170150614..170150632
+
Hg19::chr3:170150675..170150707,+p6@CLDN11
Hg19::chr3:170150778..170150789,+p13@CLDN11
Hg19::chr3:170150980..170151004,+p12@CLDN11
Hg19::chr3:170151051..170151075,+p10@CLDN11
Hg19::chr3:170151355..170151372,+p8@CLDN11
Hg19::chr3:170151409..170151477,+p5@CLDN11


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
cell layer3.18e-32312
epithelium5.11e-31309
organism subdivision3.94e-27365
anatomical cluster3.90e-25286
anatomical conduit1.04e-24241
tube7.70e-21194
somite1.01e-2083
paraxial mesoderm1.01e-2083
presomitic mesoderm1.01e-2083
presumptive segmental plate1.01e-2083
trunk paraxial mesoderm1.01e-2083
presumptive paraxial mesoderm1.01e-2083
trunk mesenchyme1.05e-20143
multi-tissue structure1.37e-20347
dermomyotome1.34e-1970
vasculature4.03e-1879
vascular system4.03e-1879
multilaminar epithelium3.27e-1782
skeletal muscle tissue2.22e-1661
striated muscle tissue2.22e-1661
myotome2.22e-1661
muscle tissue4.61e-1663
musculature4.61e-1663
musculature of body4.61e-1663
multi-cellular organism5.56e-14659
neural plate6.55e-1486
presumptive neural plate6.55e-1486
vessel7.08e-1469
epithelial tube1.67e-13118
unilaminar epithelium2.09e-13138
anatomical system3.59e-13625
splanchnic layer of lateral plate mesoderm3.87e-1384
anatomical group6.43e-13626
regional part of brain1.10e-1259
cardiovascular system1.40e-12110
trunk1.52e-12216
circulatory system2.86e-12113
neural tube3.22e-1257
neural rod3.22e-1257
future spinal cord3.22e-1257
neural keel3.22e-1257
neurectoderm5.17e-1290
blood vessel3.74e-1160
epithelial tube open at both ends3.74e-1160
blood vasculature3.74e-1160
vascular cord3.74e-1160
head4.97e-11123
central nervous system4.36e-1082
anterior region of body5.42e-10129
craniocervical region5.42e-10129
pre-chordal neural plate5.52e-1061
regional part of nervous system5.80e-1094
nervous system5.80e-1094
brain6.07e-1069
future brain6.07e-1069
embryo9.56e-09612
ectoderm-derived structure1.07e-08169
embryonic structure1.13e-08605
developing anatomical structure1.13e-08605
germ layer1.31e-08604
embryonic tissue1.31e-08604
presumptive structure1.31e-08604
epiblast (generic)1.31e-08604
organ part1.66e-08219
artery5.09e-0842
arterial blood vessel5.09e-0842
arterial system5.09e-0842
anterior neural tube7.47e-0842
regional part of forebrain9.02e-0841
forebrain9.02e-0841
future forebrain9.02e-0841
ectoderm9.73e-08173
presumptive ectoderm9.73e-08173
systemic artery1.92e-0733
systemic arterial system1.92e-0733
mesenchyme3.37e-07238
entire embryonic mesenchyme3.37e-07238
gray matter6.68e-0734
brain grey matter6.68e-0734


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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