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Coexpression cluster:C3273: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.93e-09!106;DOID:14566!4.37e-08!239;DOID:162!5.25e-08!235;DOID:0050687!1.75e-07!143
|ontology_enrichment_disease=DOID:305!1.93e-09!106;DOID:14566!4.37e-08!239;DOID:162!5.25e-08!235;DOID:0050687!1.75e-07!143
|ontology_enrichment_uberon=UBERON:0000055!1.07e-11!69;UBERON:0001981!1.39e-10!60;UBERON:0007500!1.39e-10!60;UBERON:0004537!1.39e-10!60;UBERON:0006965!1.39e-10!60;UBERON:0001637!9.28e-10!42;UBERON:0003509!9.28e-10!42;UBERON:0004572!9.28e-10!42;UBERON:0000490!1.21e-09!138;UBERON:0002049!1.42e-09!79;UBERON:0007798!1.42e-09!79;UBERON:0003914!1.26e-07!118;UBERON:0000480!2.12e-07!626;UBERON:0004573!2.76e-07!33;UBERON:0004571!2.76e-07!33;UBERON:0004111!3.44e-07!241;UBERON:0005256!3.61e-07!143;UBERON:0000483!3.78e-07!309;UBERON:0000467!3.89e-07!625;UBERON:0000119!4.16e-07!312
|ontology_enrichment_uberon=UBERON:0000055!1.07e-11!69;UBERON:0001981!1.39e-10!60;UBERON:0007500!1.39e-10!60;UBERON:0004537!1.39e-10!60;UBERON:0006965!1.39e-10!60;UBERON:0001637!9.28e-10!42;UBERON:0003509!9.28e-10!42;UBERON:0004572!9.28e-10!42;UBERON:0000490!1.21e-09!138;UBERON:0002049!1.42e-09!79;UBERON:0007798!1.42e-09!79;UBERON:0003914!1.26e-07!118;UBERON:0000480!2.12e-07!626;UBERON:0004573!2.76e-07!33;UBERON:0004571!2.76e-07!33;UBERON:0004111!3.44e-07!241;UBERON:0005256!3.61e-07!143;UBERON:0000483!3.78e-07!309;UBERON:0000467!3.89e-07!625;UBERON:0000119!4.16e-07!312
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324039915174307!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00436018374321613!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320883379361278!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460547107591939!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268835959084821!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00613730029412916!YY1#7528;3:4.91117074985386:0.00844145534180826:0.032827567561927!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0108997765716542
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}}
}}

Revision as of 13:42, 5 September 2012


Full id: C3273_osteosarcoma_endometrial_embryonic_astrocytoma_mucinous_Myoblast_prostate



Phase1 CAGE Peaks

Hg19::chr12:27485762..27485776,+p3@ARNTL2
Hg19::chr12:27485785..27485816,+p1@ARNTL2
Hg19::chr12:27485823..27485868,+p2@ARNTL2


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
epithelial cell1.15e-16254
embryonic cell6.06e-14248
endo-epithelial cell4.59e-0943
animal cell5.56e-09679
eukaryotic cell5.56e-09679
squamous epithelial cell7.12e-0962
mesodermal cell2.08e-08119
endodermal cell2.75e-0859
vascular associated smooth muscle cell1.48e-0732
endothelial cell of vascular tree3.60e-0724
Uber Anatomy
Ontology termp-valuen
vessel1.07e-1169
blood vessel1.39e-1060
epithelial tube open at both ends1.39e-1060
blood vasculature1.39e-1060
vascular cord1.39e-1060
artery9.28e-1042
arterial blood vessel9.28e-1042
arterial system9.28e-1042
unilaminar epithelium1.21e-09138
vasculature1.42e-0979
vascular system1.42e-0979
epithelial tube1.26e-07118
anatomical group2.12e-07626
systemic artery2.76e-0733
systemic arterial system2.76e-0733
anatomical conduit3.44e-07241
trunk mesenchyme3.61e-07143
epithelium3.78e-07309
anatomical system3.89e-07625
cell layer4.16e-07312
Disease
Ontology termp-valuen
carcinoma1.93e-09106
disease of cellular proliferation4.37e-08239
cancer5.25e-08235
cell type cancer1.75e-07143


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
E2F1#186934.907389214879320.008460985347239390.0324039915174307
E2F4#1874312.66806031528440.0004917987006298980.00436018374321613
E2F6#187635.017155731697390.00791769806886330.0320883379361278
ELF1#199734.258097958807540.01295179875054610.0460547107591939
NFKB1#479035.488063424193840.006049381815655430.0268835959084821
TFAP2C#7022310.80922860986020.0007916746575753130.00613730029412916
YY1#752834.911170749853860.008441455341808260.032827567561927
ZNF263#1012738.221841637010680.001799043925565870.0108997765716542



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.