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Coexpression cluster:C4574: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281089074265114
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281089074265114
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Revision as of 16:49, 26 November 2012


Full id: C4574_melanoma_adipose_mature_Fibroblast_mesenchymal_Chondrocyte_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr6:148829628..148829642,+p13@SASH1
Hg19::chr6:148829699..148829775,+p5@SASH1
Hg19::chr6:148829780..148829823,+p6@SASH1


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
fibroblast2.49e-1376
skin fibroblast3.98e-1223
non-terminally differentiated cell1.40e-09106
fat cell1.38e-0815
Uber Anatomy
Ontology termp-valuen
adult organism3.19e-23114
neural tube1.39e-1556
neural rod1.39e-1556
future spinal cord1.39e-1556
neural keel1.39e-1556
structure with developmental contribution from neural crest9.97e-15132
neurectoderm1.26e-1486
regional part of nervous system9.49e-1453
regional part of brain9.49e-1453
neural plate1.55e-1382
presumptive neural plate1.55e-1382
nervous system1.22e-1189
brain3.81e-1168
future brain3.81e-1168
central nervous system4.68e-1181
regional part of forebrain1.42e-1041
forebrain1.42e-1041
anterior neural tube1.42e-1041
future forebrain1.42e-1041
ecto-epithelium1.51e-10104
ectoderm-derived structure1.69e-10171
ectoderm1.69e-10171
presumptive ectoderm1.69e-10171
integument2.36e-1046
integumental system2.36e-1046
surface structure2.09e-0999
skin of body2.25e-0941
telencephalon8.76e-0934
brain grey matter1.43e-0834
gray matter1.43e-0834
multi-cellular organism1.48e-08656
dense mesenchyme tissue1.69e-0873
paraxial mesoderm3.44e-0872
presumptive paraxial mesoderm3.44e-0872
multi-tissue structure4.10e-08342
somite6.15e-0871
presomitic mesoderm6.15e-0871
presumptive segmental plate6.15e-0871
dermomyotome6.15e-0871
trunk paraxial mesoderm6.15e-0871
regional part of telencephalon7.84e-0832
cerebral hemisphere9.78e-0832
pre-chordal neural plate2.10e-0761
tissue3.47e-07773
muscle tissue4.73e-0764
musculature4.73e-0764
musculature of body4.73e-0764


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)

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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#1066435.360256373075030.0064925092527670.0281089074265114



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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