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Coexpression cluster:C2946: Difference between revisions

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|id=C2946
|id=C2946
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:305!7.15e-10!106;DOID:299!5.13e-08!25
|ontology_enrichment_disease=DOID:305!1.75e-13!106;DOID:299!7.39e-12!25;DOID:0050687!4.84e-08!143
|ontology_enrichment_uberon=UBERON:0007023!1.58e-24!115;UBERON:0003080!6.78e-21!42;UBERON:0002780!9.42e-21!41;UBERON:0001890!9.42e-21!41;UBERON:0006240!9.42e-21!41;UBERON:0001893!2.87e-18!34;UBERON:0002020!1.29e-17!34;UBERON:0003528!1.29e-17!34;UBERON:0002791!1.48e-17!33;UBERON:0001049!1.77e-17!57;UBERON:0005068!1.77e-17!57;UBERON:0006241!1.77e-17!57;UBERON:0007135!1.77e-17!57;UBERON:0001869!1.88e-17!32;UBERON:0002619!6.08e-17!22;UBERON:0001950!1.75e-15!20;UBERON:0002616!6.19e-15!59;UBERON:0000062!6.62e-15!511;UBERON:0003056!5.02e-14!61;UBERON:0000956!1.52e-13!25;UBERON:0000203!1.52e-13!25;UBERON:0004921!2.17e-13!129;UBERON:0004185!2.17e-13!129;UBERON:0001017!2.30e-13!82;UBERON:0000955!2.45e-13!69;UBERON:0006238!2.45e-13!69;UBERON:0004119!5.00e-13!169;UBERON:0000925!5.00e-13!169;UBERON:0006595!5.00e-13!169;UBERON:0002346!6.65e-13!90;UBERON:0005743!7.33e-13!86;UBERON:0003075!2.26e-12!86;UBERON:0007284!2.26e-12!86;UBERON:0000073!5.89e-12!94;UBERON:0001016!5.89e-12!94;UBERON:0002050!1.27e-11!605;UBERON:0005423!1.27e-11!605;UBERON:0001007!1.31e-11!155;UBERON:0001555!1.31e-11!155;UBERON:0007026!1.31e-11!155;UBERON:0000923!2.62e-11!604;UBERON:0005291!2.62e-11!604;UBERON:0006598!2.62e-11!604;UBERON:0002532!2.62e-11!604;UBERON:0000922!2.90e-11!612;UBERON:0000467!9.75e-11!625;UBERON:0000480!1.40e-10!626;UBERON:0000468!1.57e-10!659;UBERON:0000064!5.45e-10!219;UBERON:0000481!6.08e-10!347;UBERON:0005409!7.77e-10!35;UBERON:0000160!8.78e-10!27;UBERON:0000077!1.59e-09!130;UBERON:0001041!3.05e-09!98;UBERON:0000153!5.62e-08!129;UBERON:0007811!5.62e-08!129;UBERON:0001737!1.78e-07!9;UBERON:0000033!1.96e-07!123;UBERON:0002108!3.46e-07!14;UBERON:0001871!5.76e-07!7;UBERON:0001557!9.89e-07!19
|ontology_enrichment_uberon=UBERON:0002780!8.38e-26!41;UBERON:0001890!8.38e-26!41;UBERON:0003080!8.38e-26!41;UBERON:0006240!8.38e-26!41;UBERON:0007023!4.54e-25!114;UBERON:0001893!6.78e-25!34;UBERON:0003528!3.15e-24!34;UBERON:0002020!3.15e-24!34;UBERON:0011216!7.20e-24!223;UBERON:0001869!7.95e-24!32;UBERON:0002619!1.41e-23!22;UBERON:0002791!2.98e-23!32;UBERON:0001049!1.10e-22!56;UBERON:0005068!1.10e-22!56;UBERON:0006241!1.10e-22!56;UBERON:0007135!1.10e-22!56;UBERON:0000073!2.04e-22!53;UBERON:0002616!2.04e-22!53;UBERON:0001950!1.76e-21!20;UBERON:0000956!1.01e-19!25;UBERON:0000203!1.01e-19!25;UBERON:0000955!3.14e-17!68;UBERON:0006238!3.14e-17!68;UBERON:0003056!1.33e-15!61;UBERON:0001017!2.02e-15!81;UBERON:0002346!1.67e-14!86;UBERON:0001016!1.76e-14!89;UBERON:0003075!1.39e-13!82;UBERON:0007284!1.39e-13!82;UBERON:0000062!5.11e-13!503;UBERON:0000477!5.74e-13!373;UBERON:0000481!3.68e-12!342;UBERON:0000064!8.59e-12!218;UBERON:0004921!1.10e-10!118;UBERON:0010371!6.99e-10!104;UBERON:0001737!1.76e-09!9;UBERON:0004119!1.93e-09!160;UBERON:0000925!1.93e-09!160;UBERON:0006595!1.93e-09!160;UBERON:0001007!2.52e-09!145;UBERON:0001555!2.52e-09!145;UBERON:0007026!2.52e-09!145;UBERON:0010314!4.85e-09!132;UBERON:0000922!6.87e-09!592;UBERON:0000025!1.03e-08!192;UBERON:0001871!3.04e-08!6;UBERON:0000468!9.59e-08!656;UBERON:0004121!1.57e-07!171;UBERON:0000924!1.57e-07!171;UBERON:0006601!1.57e-07!171;UBERON:0000200!1.93e-07!6;UBERON:0000467!2.26e-07!624;UBERON:0005423!2.32e-07!581;UBERON:0000480!2.75e-07!625;UBERON:0001557!2.83e-07!19;UBERON:0005409!2.91e-07!25;UBERON:0004111!3.93e-07!240;UBERON:0002420!3.98e-07!9;UBERON:0007245!3.98e-07!9;UBERON:0010009!3.98e-07!9;UBERON:0010011!3.98e-07!9;UBERON:0000454!3.98e-07!9;UBERON:0000160!4.04e-07!17;UBERON:0001041!5.10e-07!87;UBERON:0000065!6.33e-07!54;UBERON:0000349!7.38e-07!5;UBERON:0008947!9.78e-07!38;UBERON:0003258!9.78e-07!38
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268903363820355!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106889386156431!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032354447657128!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245200763596907
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268903363820355!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106889386156431!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032354447657128!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245200763596907
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}}
}}

Revision as of 14:36, 19 October 2012


Full id: C2946_large_tubular_gastric_papillary_embryonic_small_cervical



Phase1 CAGE Peaks

Hg19::chr9:74764278..74764289,+p4@GDA
Hg19::chr9:74764317..74764339,+p2@GDA
Hg19::chr9:74764340..74764392,+p1@GDA
Hg19::chr9:74764397..74764408,+p3@GDA


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
regional part of forebrain8.38e-2641
forebrain8.38e-2641
anterior neural tube8.38e-2641
future forebrain8.38e-2641
adult organism4.54e-25114
telencephalon6.78e-2534
brain grey matter3.15e-2434
gray matter3.15e-2434
organ system subdivision7.20e-24223
cerebral hemisphere7.95e-2432
regional part of cerebral cortex1.41e-2322
regional part of telencephalon2.98e-2332
neural tube1.10e-2256
neural rod1.10e-2256
future spinal cord1.10e-2256
neural keel1.10e-2256
regional part of nervous system2.04e-2253
regional part of brain2.04e-2253
neocortex1.76e-2120
cerebral cortex1.01e-1925
pallium1.01e-1925
brain3.14e-1768
future brain3.14e-1768
pre-chordal neural plate1.33e-1561
central nervous system2.02e-1581
neurectoderm1.67e-1486
nervous system1.76e-1489
neural plate1.39e-1382
presumptive neural plate1.39e-1382
organ5.11e-13503
anatomical cluster5.74e-13373
multi-tissue structure3.68e-12342
organ part8.59e-12218
subdivision of digestive tract1.10e-10118
ecto-epithelium6.99e-10104
larynx1.76e-099
endoderm-derived structure1.93e-09160
endoderm1.93e-09160
presumptive endoderm1.93e-09160
digestive system2.52e-09145
digestive tract2.52e-09145
primitive gut2.52e-09145
structure with developmental contribution from neural crest4.85e-09132
embryo6.87e-09592
tube1.03e-08192
temporal lobe3.04e-086
multi-cellular organism9.59e-08656
ectoderm-derived structure1.57e-07171
ectoderm1.57e-07171
presumptive ectoderm1.57e-07171
gyrus1.93e-076
anatomical system2.26e-07624
developing anatomical structure2.32e-07581
anatomical group2.75e-07625
upper respiratory tract2.83e-0719
gastrointestinal system2.91e-0725
anatomical conduit3.93e-07240
basal ganglion3.98e-079
nuclear complex of neuraxis3.98e-079
aggregate regional part of brain3.98e-079
collection of basal ganglia3.98e-079
cerebral subcortex3.98e-079
intestine4.04e-0717
foregut5.10e-0787
respiratory tract6.33e-0754
limbic system7.38e-075
respiratory primordium9.78e-0738
endoderm of foregut9.78e-0738
Disease
Ontology termp-valuen
carcinoma1.75e-13106
adenocarcinoma7.39e-1225
cell type cancer4.84e-08143


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#105147.971147625824820.0002476385788090830.00268903363820355
E2F1#186944.907389214879320.001724022357361790.0106889386156431
TAF1#687243.343046285745290.008005664898701650.032354447657128
TBP#690843.706770687096390.005296377814784350.0245200763596907



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2946&oldid=2249119"