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Coexpression cluster:C3266: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278594508340414
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278594508340414
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}}
}}

Revision as of 16:01, 26 November 2012


Full id: C3266_uterus_aorta_smooth_colon_Olfactory_Fibroblast_dura



Phase1 CAGE Peaks

Hg19::chr12:2162144..2162196,+p1@CACNA1C
Hg19::chr12:2162419..2162431,+p5@CACNA1C
Hg19::chr12:2162447..2162462,+p3@CACNA1C


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
fibroblast9.36e-1076
skin fibroblast9.41e-0923
Uber Anatomy
Ontology termp-valuen
adult organism4.60e-31114
neural tube1.78e-2856
neural rod1.78e-2856
future spinal cord1.78e-2856
neural keel1.78e-2856
regional part of nervous system9.08e-2753
regional part of brain9.08e-2753
central nervous system2.59e-2581
brain5.01e-2568
future brain5.01e-2568
nervous system5.68e-2389
structure with developmental contribution from neural crest1.18e-20132
regional part of forebrain1.54e-2041
forebrain1.54e-2041
anterior neural tube1.54e-2041
future forebrain1.54e-2041
telencephalon4.56e-2034
brain grey matter5.23e-2034
gray matter5.23e-2034
cerebral hemisphere1.27e-1932
neural plate1.41e-1982
presumptive neural plate1.41e-1982
regional part of telencephalon3.17e-1932
neurectoderm5.02e-1986
regional part of cerebral cortex1.52e-1822
neocortex4.13e-1720
cerebral cortex4.04e-1625
pallium4.04e-1625
ecto-epithelium1.98e-15104
ectoderm-derived structure2.55e-15171
ectoderm2.55e-15171
presumptive ectoderm2.55e-15171
organ system subdivision7.65e-12223
pre-chordal neural plate1.44e-1061
multi-cellular organism3.95e-09656
multi-tissue structure4.38e-09342
posterior neural tube4.43e-0915
chordal neural plate4.43e-0915
segmental subdivision of hindbrain1.78e-0712
hindbrain1.78e-0712
presumptive hindbrain1.78e-0712
integument3.15e-0746
integumental system3.15e-0746
anatomical system4.15e-07624
anatomical group5.28e-07625
organ part5.56e-07218


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#1066435.360256373075030.0064925092527670.0278594508340414



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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