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Coexpression cluster:C3985: Difference between revisions

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|ontology_enrichment_disease=DOID:14566!3.62e-08!239;DOID:0050687!7.64e-08!143;DOID:162!1.27e-07!235
|ontology_enrichment_disease=DOID:14566!3.62e-08!239;DOID:0050687!7.64e-08!143;DOID:162!1.27e-07!235
|ontology_enrichment_uberon=UBERON:0000475!6.25e-11!365;UBERON:0003102!1.89e-10!95;UBERON:0002100!2.16e-10!216;UBERON:0003104!1.39e-08!238;UBERON:0009142!1.39e-08!238;UBERON:0005256!5.08e-08!143;UBERON:0002199!2.39e-07!45;UBERON:0002416!2.39e-07!45;UBERON:0000481!3.78e-07!347;UBERON:0000914!5.13e-07!83;UBERON:0002329!5.13e-07!83;UBERON:0003077!5.13e-07!83;UBERON:0003059!5.13e-07!83;UBERON:0007282!5.13e-07!83;UBERON:0009618!5.13e-07!83;UBERON:0007285!5.13e-07!83;UBERON:0000486!7.13e-07!82;UBERON:0004119!7.71e-07!169;UBERON:0000925!7.71e-07!169;UBERON:0006595!7.71e-07!169
|ontology_enrichment_uberon=UBERON:0000475!6.25e-11!365;UBERON:0003102!1.89e-10!95;UBERON:0002100!2.16e-10!216;UBERON:0003104!1.39e-08!238;UBERON:0009142!1.39e-08!238;UBERON:0005256!5.08e-08!143;UBERON:0002199!2.39e-07!45;UBERON:0002416!2.39e-07!45;UBERON:0000481!3.78e-07!347;UBERON:0000914!5.13e-07!83;UBERON:0002329!5.13e-07!83;UBERON:0003077!5.13e-07!83;UBERON:0003059!5.13e-07!83;UBERON:0007282!5.13e-07!83;UBERON:0009618!5.13e-07!83;UBERON:0007285!5.13e-07!83;UBERON:0000486!7.13e-07!82;UBERON:0004119!7.71e-07!169;UBERON:0000925!7.71e-07!169;UBERON:0006595!7.71e-07!169
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.0012969323658017!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115295041026272!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325724077068943!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322636156306677!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320990182192114!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167631864360014!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444635863924532!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156948297288587!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370792814168626!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00643181933872549
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}}
}}

Revision as of 14:28, 5 September 2012


Full id: C3985_Preadipocyte_squamous_mesenchymal_Prostate_cholangiocellular_Small_nasal



Phase1 CAGE Peaks

Hg19::chr1:52521359..52521378,-p4@TXNDC12
Hg19::chr1:52521381..52521400,-p2@TXNDC12
Hg19::chr1:52521417..52521448,-p5@TXNDC12


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>disease_data<br>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.99e-16180
animal cell7.89e-14679
eukaryotic cell7.89e-14679
fibroblast1.29e-1075
embryonic cell2.39e-09248
endodermal cell7.00e-0959
fat cell1.21e-0815
muscle precursor cell1.69e-0857
myoblast1.69e-0857
multi-potent skeletal muscle stem cell1.69e-0857
muscle cell3.42e-0854
endo-epithelial cell1.47e-0743
smooth muscle cell1.63e-0742
smooth muscle myoblast1.63e-0742
contractile cell8.06e-0759
Uber Anatomy
Ontology termp-valuen
organism subdivision6.25e-11365
surface structure1.89e-1095
trunk2.16e-10216
mesenchyme1.39e-08238
entire embryonic mesenchyme1.39e-08238
trunk mesenchyme5.08e-08143
integument2.39e-0745
integumental system2.39e-0745
multi-tissue structure3.78e-07347
somite5.13e-0783
paraxial mesoderm5.13e-0783
presomitic mesoderm5.13e-0783
presumptive segmental plate5.13e-0783
trunk paraxial mesoderm5.13e-0783
presumptive paraxial mesoderm5.13e-0783
multilaminar epithelium7.13e-0782
endoderm-derived structure7.71e-07169
endoderm7.71e-07169
presumptive endoderm7.71e-07169
Disease
Ontology termp-valuen
disease of cellular proliferation3.62e-08239
cell type cancer7.64e-08143
cancer1.27e-07235


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
ATF3#467322.46317452600878.81932387510763e-050.0012969323658017
CEBPB#105137.971147625824820.001974187055288560.0115295041026272
E2F1#186934.907389214879320.008460985347239390.0325724077068943
E2F6#187635.017155731697390.00791769806886330.0322636156306677
EGR1#195834.988179094810140.008056488137383440.0320990182192114
EP300#203336.77394172622320.003216880500103790.0167631864360014
JUN#3725312.51282919233630.0005103313992726250.00444635863924532
JUND#372736.994663941871030.002921845042734990.0156948297288587
SIX5#147912211.3911435703060.009873820081429030.0370792814168626
STAT3#6774310.51946499715420.0008589184530415310.00643181933872549



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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