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Coexpression cluster:C2192: Difference between revisions

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|id=C2192
|id=C2192
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:305!8.42e-10!106
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.35e-34!115;UBERON:0001049!1.33e-23!57;UBERON:0005068!1.33e-23!57;UBERON:0006241!1.33e-23!57;UBERON:0007135!1.33e-23!57;UBERON:0001017!6.00e-19!82;UBERON:0002616!2.02e-18!59;UBERON:0000955!4.94e-18!69;UBERON:0006238!4.94e-18!69;UBERON:0005743!4.97e-18!86;UBERON:0003080!2.02e-16!42;UBERON:0002780!1.13e-15!41;UBERON:0001890!1.13e-15!41;UBERON:0006240!1.13e-15!41;UBERON:0002020!1.73e-15!34;UBERON:0003528!1.73e-15!34;UBERON:0001893!6.09e-15!34;UBERON:0000073!8.76e-15!94;UBERON:0001016!8.76e-15!94;UBERON:0002791!2.16e-14!33;UBERON:0004921!1.03e-13!129;UBERON:0004185!1.03e-13!129;UBERON:0001869!1.25e-13!32;UBERON:0003075!9.47e-13!86;UBERON:0007284!9.47e-13!86;UBERON:0000153!3.85e-12!129;UBERON:0007811!3.85e-12!129;UBERON:0001007!4.46e-12!155;UBERON:0001555!4.46e-12!155;UBERON:0007026!4.46e-12!155;UBERON:0002619!5.85e-12!22;UBERON:0002346!1.43e-11!90;UBERON:0005409!5.49e-11!35;UBERON:0001950!1.78e-10!20;UBERON:0000033!3.89e-10!123;UBERON:0004119!4.25e-10!169;UBERON:0000925!4.25e-10!169;UBERON:0006595!4.25e-10!169;UBERON:0000956!7.03e-10!25;UBERON:0000203!7.03e-10!25;UBERON:0000077!1.54e-09!130;UBERON:0003056!7.07e-09!61;UBERON:0002298!8.17e-09!8;UBERON:0003076!1.78e-08!15;UBERON:0003057!1.78e-08!15;UBERON:0000062!1.00e-07!511;UBERON:0002308!1.68e-07!9;UBERON:0000125!1.68e-07!9;UBERON:0004111!1.90e-07!241;UBERON:0001041!3.06e-07!98;UBERON:0000025!3.53e-07!194;UBERON:0000160!3.76e-07!27
|ontology_enrichment_uberon=UBERON:0001049!8.89e-35!56;UBERON:0005068!8.89e-35!56;UBERON:0006241!8.89e-35!56;UBERON:0007135!8.89e-35!56;UBERON:0007023!7.15e-33!114;UBERON:0000073!3.07e-32!53;UBERON:0002616!3.07e-32!53;UBERON:0011216!8.77e-30!223;UBERON:0000955!1.43e-24!68;UBERON:0006238!1.43e-24!68;UBERON:0003528!3.77e-23!34;UBERON:0002020!3.77e-23!34;UBERON:0001893!4.76e-23!34;UBERON:0005409!7.19e-23!25;UBERON:0002780!1.21e-22!41;UBERON:0001890!1.21e-22!41;UBERON:0003080!1.21e-22!41;UBERON:0006240!1.21e-22!41;UBERON:0001017!1.71e-22!81;UBERON:0003075!5.22e-21!82;UBERON:0007284!5.22e-21!82;UBERON:0002791!4.74e-20!32;UBERON:0001869!7.31e-20!32;UBERON:0002346!1.24e-19!86;UBERON:0000160!2.07e-19!17;UBERON:0001016!2.15e-19!89;UBERON:0002619!6.11e-19!22;UBERON:0001950!3.65e-18!20;UBERON:0000956!2.57e-16!25;UBERON:0000203!2.57e-16!25;UBERON:0000477!8.29e-16!373;UBERON:0000481!1.07e-15!342;UBERON:0010371!8.90e-15!104;UBERON:0000025!1.10e-13!192;UBERON:0002298!1.63e-13!6;UBERON:0003076!1.75e-13!15;UBERON:0003057!1.75e-13!15;UBERON:0003056!2.27e-13!61;UBERON:0004921!1.64e-12!118;UBERON:0000059!2.61e-11!11;UBERON:0004733!4.91e-11!12;UBERON:0002028!4.91e-11!12;UBERON:0007277!4.91e-11!12;UBERON:0004111!7.14e-11!240;UBERON:0010314!7.81e-11!132;UBERON:0001007!2.53e-10!145;UBERON:0001555!2.53e-10!145;UBERON:0007026!2.53e-10!145;UBERON:0004732!4.45e-10!13;UBERON:0000064!1.67e-09!218;UBERON:0000200!3.33e-09!6;UBERON:0002108!3.65e-09!4;UBERON:0000062!4.00e-09!503;UBERON:0004907!7.21e-09!5;UBERON:0004119!1.39e-08!160;UBERON:0000925!1.39e-08!160;UBERON:0006595!1.39e-08!160;UBERON:0000125!2.27e-08!9;UBERON:0002308!2.27e-08!9;UBERON:0001871!2.48e-08!6;UBERON:0001896!7.08e-08!3;UBERON:0005290!7.08e-08!3;UBERON:0010096!7.08e-08!3;UBERON:0004121!1.14e-07!171;UBERON:0000924!1.14e-07!171;UBERON:0006601!1.14e-07!171;UBERON:0001155!2.20e-07!9;UBERON:0000988!2.62e-07!3;UBERON:0002294!6.58e-07!9;UBERON:0001173!6.58e-07!9;UBERON:0004912!6.58e-07!9
|tf_chipseq_enrich=HNF4A#3172;3:17.3492177722153:0.000312564155748275:0.0032142465401924!HNF4G#3174;3:21.5650668948351:0.000163803242129261:0.00203563146177271
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}}
}}

Revision as of 12:10, 19 October 2012


Full id: C2192_small_signet_gastric_adenocarcinoma_colon_bile_duodenum



Phase1 CAGE Peaks

Hg19::chr12:12223867..12223883,+p1@BCL2L14
Hg19::chr2:241544820..241544829,+p6@GPR35
Hg19::chr2:241544834..241544861,+p2@GPR35
Hg19::chr2:241544866..241544882,+p4@GPR35


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><br>


Uber Anatomy
Ontology termp-valuen
neural tube8.89e-3556
neural rod8.89e-3556
future spinal cord8.89e-3556
neural keel8.89e-3556
adult organism7.15e-33114
regional part of nervous system3.07e-3253
regional part of brain3.07e-3253
organ system subdivision8.77e-30223
brain1.43e-2468
future brain1.43e-2468
brain grey matter3.77e-2334
gray matter3.77e-2334
telencephalon4.76e-2334
gastrointestinal system7.19e-2325
regional part of forebrain1.21e-2241
forebrain1.21e-2241
anterior neural tube1.21e-2241
future forebrain1.21e-2241
central nervous system1.71e-2281
neural plate5.22e-2182
presumptive neural plate5.22e-2182
regional part of telencephalon4.74e-2032
cerebral hemisphere7.31e-2032
neurectoderm1.24e-1986
intestine2.07e-1917
nervous system2.15e-1989
regional part of cerebral cortex6.11e-1922
neocortex3.65e-1820
cerebral cortex2.57e-1625
pallium2.57e-1625
anatomical cluster8.29e-16373
multi-tissue structure1.07e-15342
ecto-epithelium8.90e-15104
tube1.10e-13192
brainstem1.63e-136
posterior neural tube1.75e-1315
chordal neural plate1.75e-1315
pre-chordal neural plate2.27e-1361
subdivision of digestive tract1.64e-12118
large intestine2.61e-1111
segmental subdivision of hindbrain4.91e-1112
hindbrain4.91e-1112
presumptive hindbrain4.91e-1112
anatomical conduit7.14e-11240
structure with developmental contribution from neural crest7.81e-11132
digestive system2.53e-10145
digestive tract2.53e-10145
primitive gut2.53e-10145
segmental subdivision of nervous system4.45e-1013
organ part1.67e-09218
gyrus3.33e-096
small intestine3.65e-094
organ4.00e-09503
lower digestive tract7.21e-095
endoderm-derived structure1.39e-08160
endoderm1.39e-08160
presumptive endoderm1.39e-08160
neural nucleus2.27e-089
nucleus of brain2.27e-089
temporal lobe2.48e-086
medulla oblongata7.08e-083
myelencephalon7.08e-083
future myelencephalon7.08e-083
ectoderm-derived structure1.14e-07171
ectoderm1.14e-07171
presumptive ectoderm1.14e-07171
colon2.20e-079
pons2.62e-073
biliary system6.58e-079
biliary tree6.58e-079
biliary bud6.58e-079


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
HNF4A#3172317.34921777221530.0003125641557482750.0032142465401924
HNF4G#3174321.56506689483510.0001638032421292610.00203563146177271



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.