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Coexpression cluster:C3307: Difference between revisions

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|ontology_enrichment_disease=DOID:162!1.55e-17!235;DOID:14566!2.14e-16!239;DOID:0050687!7.62e-16!143;DOID:305!2.67e-11!106;DOID:0050686!6.94e-08!137
|ontology_enrichment_disease=DOID:162!1.55e-17!235;DOID:14566!2.14e-16!239;DOID:0050687!7.62e-16!143;DOID:305!2.67e-11!106;DOID:0050686!6.94e-08!137
|ontology_enrichment_uberon=UBERON:0002368!1.41e-08!35;UBERON:0002107!1.55e-08!19;UBERON:0006925!1.55e-08!19;UBERON:0008836!1.55e-08!19;UBERON:0008835!7.38e-08!22;UBERON:0003894!7.38e-08!22;UBERON:0000949!1.25e-07!45;UBERON:0009497!1.31e-07!25;UBERON:0000015!1.31e-07!25;UBERON:0002423!1.31e-07!25;UBERON:0006235!1.31e-07!25;UBERON:0004161!1.31e-07!25;UBERON:0009854!2.88e-07!23;UBERON:0003929!3.65e-07!54;UBERON:0005057!5.23e-07!26
|ontology_enrichment_uberon=UBERON:0002368!1.41e-08!35;UBERON:0002107!1.55e-08!19;UBERON:0006925!1.55e-08!19;UBERON:0008836!1.55e-08!19;UBERON:0008835!7.38e-08!22;UBERON:0003894!7.38e-08!22;UBERON:0000949!1.25e-07!45;UBERON:0009497!1.31e-07!25;UBERON:0000015!1.31e-07!25;UBERON:0002423!1.31e-07!25;UBERON:0006235!1.31e-07!25;UBERON:0004161!1.31e-07!25;UBERON:0009854!2.88e-07!23;UBERON:0003929!3.65e-07!54;UBERON:0005057!5.23e-07!26
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.031951528995982!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167056726443409!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00895498541337993!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000735190136731064!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199150070756!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245128066245723!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136285008769088!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275793418036465!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239202376454443!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245737127445516!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000938520328286098!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00628169680229137!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.01397921409607
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618,0.0133429,0.000324864,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 13:38, 5 September 2012


Full id: C3307_smallcell_Hepatocyte_somatostatinoma_liver_medulloblastoma_acute_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr12:57849247..57849272,+p3@INHBE
Hg19::chr12:57849281..57849299,+p4@INHBE
Hg19::chr12:57849300..57849316,+p2@INHBE


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
metabolising cell2.40e-0712
endopolyploid cell2.40e-0712
parenchymal cell2.40e-0712
polyploid cell2.40e-0712
hepatocyte2.40e-0712
Uber Anatomy
Ontology termp-valuen
endocrine gland1.41e-0835
liver1.55e-0819
digestive gland1.55e-0819
liver bud1.55e-0819
hepatic diverticulum7.38e-0822
liver primordium7.38e-0822
endocrine system1.25e-0745
epithelium of foregut-midgut junction1.31e-0725
anatomical boundary1.31e-0725
hepatobiliary system1.31e-0725
foregut-midgut junction1.31e-0725
septum transversum1.31e-0725
digestive tract diverticulum2.88e-0723
gut epithelium3.65e-0754
immune organ5.23e-0726
Disease
Ontology termp-valuen
cancer1.55e-17235
disease of cellular proliferation2.14e-16239
cell type cancer7.62e-16143
carcinoma2.67e-11106
organ system cancer6.94e-08137


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
EGR1#195834.988179094810140.008056488137383440.031951528995982
EP300#203336.77394172622320.003216880500103790.0167056726443409
FOS#235338.99795530889440.001372499272417130.00895498541337993
NANOG#79923329.24477848101273.99627955670032e-050.000735190136731064
NFYA#4800318.42558069983050.0001598135507814160.00199150070756
NFYB#4801316.75979325353650.0002123649923296180.00245128066245723
PBX3#5090321.91451268674419.49854535978121e-050.00136285008769088
SIN3A#2594235.408884726815140.006318961977991520.0275793418036465
SIX5#147912317.0867153554590.0002004060546325010.00239202376454443
SP1#666735.69838137814090.005403962701712170.0245737127445516
SP2#6668326.15353049384465.58768218891694e-050.000938520328286098
TCF12#6938310.63446490218640.0008313523990202070.00628169680229137
ZBTB7A#5134137.35190930787590.002516255860282270.01397921409607



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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