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Coexpression cluster:C3139: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3139_myeloma_gall_Smooth_mesenchymal_Fibroblast_mesothelioma_meningioma
|full_id=C3139_myeloma_gall_Smooth_mesenchymal_Fibroblast_mesothelioma_meningioma
|id=C3139
|id=C3139

Revision as of 16:00, 12 September 2012


Full id: C3139_myeloma_gall_Smooth_mesenchymal_Fibroblast_mesothelioma_meningioma



Phase1 CAGE Peaks

Hg19::chr11:314010..314046,+p2@IFITM1
Hg19::chr11:314052..314073,+p1@IFITM1
Hg19::chr11:314077..314099,+p4@IFITM1


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
adult organism2.52e-10115


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#1066435.360256373075030.0064925092527670.0278365767826977
ELF1#199734.258097958807540.01295179875054610.0460155432612697
EP300#203336.77394172622320.003216880500103790.0166890756818012
ETS1#211339.728760922202340.001085840092584840.00760029846722523
GTF2B#2959331.94382993432423.06634405746243e-050.000625846994366463
GTF2F1#2962312.73966087675770.0004835525047438590.00432748415106632
HMGN3#932438.178547723350590.001827766942164210.0108331054805453
IRF1#365937.63716375356390.002244692747297240.0127638409013435
MAX#414936.452555509007120.003721913834265510.0185791491701011
NFKB1#479035.488063424193840.006049381815655430.0268630208531501
POU2F2#545239.106124057742520.001324165192682130.00879568075803148
SIX5#147912317.0867153554590.0002004060546325010.00239011167520427
SPI1#668838.204323508522730.001810593189410520.0108813754234575
STAT1#6772320.70658749719920.0001125992441046670.00154449073483679
STAT2#6773365.26377118644073.59360517547754e-060.000118134255877148
ZBTB7A#5134137.35190930787590.002516255860282270.0139621318559143



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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