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Coexpression cluster:C3886: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3886_CD14_malignant_oral_Keratinocyte_Mallassezderived_Smooth_Small
|full_id=C3886_CD14_malignant_oral_Keratinocyte_Mallassezderived_Smooth_Small
|id=C3886
|id=C3886

Revision as of 16:52, 12 September 2012


Full id: C3886_CD14_malignant_oral_Keratinocyte_Mallassezderived_Smooth_Small



Phase1 CAGE Peaks

Hg19::chr1:158979792..158979814,+p2@IFI16
Hg19::chr1:158979851..158979865,+p5@IFI16
Hg19::chr1:158979872..158979898,+p3@IFI16


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
musculoskeletal system5.33e-20167
hematopoietic system3.47e-15102
blood island3.47e-15102
bone marrow4.26e-1580
skeletal element7.69e-15101
skeletal system7.69e-15101
hemolymphoid system2.04e-14112
bone element1.55e-1386
lateral plate mesoderm4.34e-12216
mesoderm9.65e-11448
mesoderm-derived structure9.65e-11448
presumptive mesoderm9.65e-11448
anatomical system1.07e-09625
anatomical group1.46e-09626
immune system5.94e-09115
multi-cellular organism1.28e-08659
surface structure2.46e-0895
germ layer8.81e-07604
embryonic tissue8.81e-07604
presumptive structure8.81e-07604
epiblast (generic)8.81e-07604
embryonic structure9.65e-07605
developing anatomical structure9.65e-07605


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
CEBPB#105137.971147625824820.001974187055288560.0115243486595093
EP300#203336.77394172622320.003216880500103790.0167514849696021
FOS#235338.99795530889440.001372499272417130.00897854378402584
GATA2#2624312.7449317335540.0004829527704283790.00436967031021134
JUN#3725312.51282919233630.0005103313992726250.00444339316453803
JUND#372736.994663941871030.002921845042734990.0156835367434959
MAX#414936.452555509007120.003721913834265510.0186612078222206
MYC#460935.22228187160940.007020843755740150.0294643534921541
NFKB1#479035.488063424193840.006049381815655430.0269719683847864
POU2F2#545239.106124057742520.001324165192682130.00882543002926158
SRF#6722313.79717826216780.0003806615025800190.00375268139210446
STAT1#6772320.70658749719920.0001125992441046670.00154937450000623
STAT2#6773365.26377118644073.59360517547754e-060.000118357783324408
STAT3#6774310.51946499715420.0008589184530415310.00642767156185185
USF1#739136.361499277207960.00388404057290560.0190363373876619
YY1#752834.911170749853860.008441455341808260.0329576506333874



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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