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Coexpression cluster:C4618

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Full id: C4618_rectum_skeletal_Fibroblast_aorta_skin_throat_pleomorphic



Phase1 CAGE Peaks

Hg19::chr6:56112246..56112267,-p2@COL21A1
Hg19::chr6:56112289..56112311,-p4@COL21A1
Hg19::chr6:56112323..56112385,-p1@COL21A1


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.21e-40114
neural tube2.38e-2756
neural rod2.38e-2756
future spinal cord2.38e-2756
neural keel2.38e-2756
central nervous system5.54e-2781
regional part of nervous system3.79e-2553
regional part of brain3.79e-2553
brain1.83e-2468
future brain1.83e-2468
neural plate4.72e-2482
presumptive neural plate4.72e-2482
neurectoderm1.18e-2386
nervous system2.09e-2389
regional part of forebrain2.07e-2041
forebrain2.07e-2041
anterior neural tube2.07e-2041
future forebrain2.07e-2041
structure with developmental contribution from neural crest4.69e-20132
ectoderm-derived structure6.59e-20171
ectoderm6.59e-20171
presumptive ectoderm6.59e-20171
organ system subdivision1.14e-18223
pre-chordal neural plate6.77e-1761
ecto-epithelium8.14e-17104
brain grey matter2.18e-1634
gray matter2.18e-1634
multi-tissue structure3.32e-16342
telencephalon3.40e-1634
regional part of telencephalon4.45e-1532
cerebral hemisphere7.08e-1532
anatomical cluster1.27e-14373
multi-cellular organism2.14e-12656
regional part of cerebral cortex4.69e-1222
cerebral cortex1.42e-1125
pallium1.42e-1125
neocortex8.49e-1120
embryo5.70e-10592
embryonic structure2.35e-09564
germ layer2.45e-09560
germ layer / neural crest2.45e-09560
embryonic tissue2.45e-09560
presumptive structure2.45e-09560
germ layer / neural crest derived structure2.45e-09560
epiblast (generic)2.45e-09560
cell layer4.64e-09309
epithelium6.36e-09306
developing anatomical structure1.44e-08581
anatomical system4.11e-08624
posterior neural tube4.28e-0815
chordal neural plate4.28e-0815
anatomical group5.22e-08625
organ9.34e-08503
vasculature of organ9.42e-0811
anatomical conduit1.21e-07240


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#1066435.360256373075030.0064925092527670.0281147347976504



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.