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Coexpression cluster:C2660: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818234119370453!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129577802888857!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000304571946455243
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818234119370453!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129577802888857!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000304571946455243
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}}
}}

Revision as of 15:38, 26 November 2012


Full id: C2660_Olfactory_mesodermal_mesenchymal_Retinal_glioblastoma_Fibroblast_basal



Phase1 CAGE Peaks

Hg19::chr2:149894968..149894986,+p5@LYPD6B
Hg19::chr2:149895005..149895022,+p6@LYPD6B
Hg19::chr2:149895029..149895054,+p3@LYPD6B
Hg19::chr2:149895062..149895085,+p4@LYPD6B


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
skin fibroblast1.40e-0823
Uber Anatomy
Ontology termp-valuen
pre-chordal neural plate7.72e-1161
pigment epithelium of eye1.74e-1011
skin of body9.93e-1041
eye7.88e-0921
visual system7.88e-0921
ectodermal placode2.85e-0831
camera-type eye3.05e-0820
simple eye3.05e-0820
immature eye3.05e-0820
ocular region3.05e-0820
eyeball of camera-type eye3.05e-0820
optic cup3.05e-0820
optic vesicle3.05e-0820
eye primordium3.05e-0820
regional part of cerebral cortex7.48e-0822
integument7.56e-0846
integumental system7.56e-0846
ecto-epithelium1.01e-07104
neural plate1.49e-0782
presumptive neural plate1.49e-0782
sense organ3.80e-0724
sensory system3.80e-0724
entire sense organ system3.80e-0724
face4.22e-0722
vasculature of eye5.69e-076
uvea5.69e-076
vasculature of head5.69e-076
neurectoderm9.58e-0786
ectoderm-derived structure9.59e-07171
ectoderm9.59e-07171
presumptive ectoderm9.59e-07171


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#1066445.360256373075030.001211145381643620.00818234119370453
RAD21#5885410.35503389545638.6948481184721e-050.00129577802888857
ZEB1#6935416.88843201754391.22862303393937e-050.000304571946455243



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.