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Coexpression cluster:C3134: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.61e-19!115;UBERON:0001049!2.74e-17!57;UBERON:0005068!2.74e-17!57;UBERON:0006241!2.74e-17!57;UBERON:0007135!2.74e-17!57;UBERON:0003075!2.05e-15!86;UBERON:0007284!2.05e-15!86;UBERON:0002616!9.77e-15!59;UBERON:0002346!2.03e-14!90;UBERON:0005743!7.78e-14!86;UBERON:0001017!1.64e-13!82;UBERON:0000073!5.28e-13!94;UBERON:0001016!5.28e-13!94;UBERON:0002298!7.00e-12!8;UBERON:0000955!1.38e-11!69;UBERON:0006238!1.38e-11!69;UBERON:0002020!8.35e-11!34;UBERON:0003528!8.35e-11!34;UBERON:0003076!2.13e-10!15;UBERON:0003057!2.13e-10!15;UBERON:0002368!4.04e-10!35;UBERON:0002780!9.44e-10!41;UBERON:0001890!9.44e-10!41;UBERON:0006240!9.44e-10!41;UBERON:0001869!1.04e-09!32;UBERON:0003080!1.91e-09!42;UBERON:0004121!5.33e-09!169;UBERON:0001893!5.41e-09!34;UBERON:0000988!5.93e-09!3;UBERON:0001896!7.54e-09!3;UBERON:0005290!7.54e-09!3;UBERON:0010096!7.54e-09!3;UBERON:0000025!9.56e-09!194;UBERON:0000924!1.31e-08!173;UBERON:0006601!1.31e-08!173;UBERON:0005057!1.41e-08!26;UBERON:0000949!1.54e-08!45;UBERON:0000483!2.18e-08!309;UBERON:0002107!3.23e-08!19;UBERON:0006925!3.23e-08!19;UBERON:0008836!3.23e-08!19;UBERON:0000119!3.37e-08!312;UBERON:0001872!4.14e-08!5;UBERON:0000153!5.42e-08!129;UBERON:0007811!5.42e-08!129;UBERON:0002791!6.76e-08!33;UBERON:0001950!7.42e-08!20;UBERON:0004111!1.05e-07!241;UBERON:0004733!1.18e-07!12;UBERON:0002028!1.18e-07!12;UBERON:0007277!1.18e-07!12;UBERON:0002308!3.51e-07!9;UBERON:0000125!3.51e-07!9;UBERON:0000033!3.83e-07!123;UBERON:0000477!4.52e-07!286;UBERON:0002619!4.91e-07!22;UBERON:0004732!5.28e-07!13;UBERON:0008835!6.82e-07!22;UBERON:0003894!6.82e-07!22;UBERON:0000475!7.74e-07!365;UBERON:0000481!9.42e-07!347
|ontology_enrichment_uberon=UBERON:0007023!2.61e-19!115;UBERON:0001049!2.74e-17!57;UBERON:0005068!2.74e-17!57;UBERON:0006241!2.74e-17!57;UBERON:0007135!2.74e-17!57;UBERON:0003075!2.05e-15!86;UBERON:0007284!2.05e-15!86;UBERON:0002616!9.77e-15!59;UBERON:0002346!2.03e-14!90;UBERON:0005743!7.78e-14!86;UBERON:0001017!1.64e-13!82;UBERON:0000073!5.28e-13!94;UBERON:0001016!5.28e-13!94;UBERON:0002298!7.00e-12!8;UBERON:0000955!1.38e-11!69;UBERON:0006238!1.38e-11!69;UBERON:0002020!8.35e-11!34;UBERON:0003528!8.35e-11!34;UBERON:0003076!2.13e-10!15;UBERON:0003057!2.13e-10!15;UBERON:0002368!4.04e-10!35;UBERON:0002780!9.44e-10!41;UBERON:0001890!9.44e-10!41;UBERON:0006240!9.44e-10!41;UBERON:0001869!1.04e-09!32;UBERON:0003080!1.91e-09!42;UBERON:0004121!5.33e-09!169;UBERON:0001893!5.41e-09!34;UBERON:0000988!5.93e-09!3;UBERON:0001896!7.54e-09!3;UBERON:0005290!7.54e-09!3;UBERON:0010096!7.54e-09!3;UBERON:0000025!9.56e-09!194;UBERON:0000924!1.31e-08!173;UBERON:0006601!1.31e-08!173;UBERON:0005057!1.41e-08!26;UBERON:0000949!1.54e-08!45;UBERON:0000483!2.18e-08!309;UBERON:0002107!3.23e-08!19;UBERON:0006925!3.23e-08!19;UBERON:0008836!3.23e-08!19;UBERON:0000119!3.37e-08!312;UBERON:0001872!4.14e-08!5;UBERON:0000153!5.42e-08!129;UBERON:0007811!5.42e-08!129;UBERON:0002791!6.76e-08!33;UBERON:0001950!7.42e-08!20;UBERON:0004111!1.05e-07!241;UBERON:0004733!1.18e-07!12;UBERON:0002028!1.18e-07!12;UBERON:0007277!1.18e-07!12;UBERON:0002308!3.51e-07!9;UBERON:0000125!3.51e-07!9;UBERON:0000033!3.83e-07!123;UBERON:0000477!4.52e-07!286;UBERON:0002619!4.91e-07!22;UBERON:0004732!5.28e-07!13;UBERON:0008835!6.82e-07!22;UBERON:0003894!6.82e-07!22;UBERON:0000475!7.74e-07!365;UBERON:0000481!9.42e-07!347
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}}
}}

Revision as of 14:04, 5 September 2012


Full id: C3134_small_B_rhabdomyosarcoma_gastrointestinal_hereditary_liver_hepatocellular



Phase1 CAGE Peaks

Hg19::chr11:22688593..22688606,+p14@GAS2
Hg19::chr11:22688615..22688625,+p25@GAS2
Hg19::chr11:22688630..22688642,+p13@GAS2


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><br>

Cell Type
Ontology termp-valuen
metabolising cell7.21e-0812
endopolyploid cell7.21e-0812
parenchymal cell7.21e-0812
polyploid cell7.21e-0812
hepatocyte7.21e-0812
Uber Anatomy
Ontology termp-valuen
adult organism2.61e-19115
neural tube2.74e-1757
neural rod2.74e-1757
future spinal cord2.74e-1757
neural keel2.74e-1757
neural plate2.05e-1586
presumptive neural plate2.05e-1586
regional part of brain9.77e-1559
neurectoderm2.03e-1490
central nervous system1.64e-1382
regional part of nervous system5.28e-1394
nervous system5.28e-1394
brainstem7.00e-128
brain1.38e-1169
future brain1.38e-1169
gray matter8.35e-1134
brain grey matter8.35e-1134
posterior neural tube2.13e-1015
chordal neural plate2.13e-1015
endocrine gland4.04e-1035
regional part of forebrain9.44e-1041
forebrain9.44e-1041
future forebrain9.44e-1041
cerebral hemisphere1.04e-0932
anterior neural tube1.91e-0942
ectoderm-derived structure5.33e-09169
telencephalon5.41e-0934
pons5.93e-093
medulla oblongata7.54e-093
myelencephalon7.54e-093
future myelencephalon7.54e-093
tube9.56e-09194
ectoderm1.31e-08173
presumptive ectoderm1.31e-08173
immune organ1.41e-0826
endocrine system1.54e-0845
epithelium2.18e-08309
liver3.23e-0819
digestive gland3.23e-0819
liver bud3.23e-0819
cell layer3.37e-08312
parietal lobe4.14e-085
anterior region of body5.42e-08129
craniocervical region5.42e-08129
regional part of telencephalon6.76e-0833
neocortex7.42e-0820
anatomical conduit1.05e-07241
segmental subdivision of hindbrain1.18e-0712
hindbrain1.18e-0712
presumptive hindbrain1.18e-0712
nucleus of brain3.51e-079
neural nucleus3.51e-079
head3.83e-07123
anatomical cluster4.52e-07286
regional part of cerebral cortex4.91e-0722
segmental subdivision of nervous system5.28e-0713
hepatic diverticulum6.82e-0722
liver primordium6.82e-0722
organism subdivision7.74e-07365
multi-tissue structure9.42e-07347


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
CTCF#1066435.360256373075030.0064925092527670.027835434066081
MAFF#23764237.54357099329680.0009344774015560320.00676809190992444
MAFK#7975218.06715542521990.003983674744936810.0191059426288784



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:C3134&oldid=2132956"