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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2946_large_tubular_gastric_papillary_embryonic_small_cervical
|full_id=C2946_large_tubular_gastric_papillary_embryonic_small_cervical
|id=C2946
|id=C2946

Revision as of 15:45, 12 September 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
adult organism1.58e-24115
anterior neural tube6.78e-2142
regional part of forebrain9.42e-2141
forebrain9.42e-2141
future forebrain9.42e-2141
telencephalon2.87e-1834
gray matter1.29e-1734
brain grey matter1.29e-1734
regional part of telencephalon1.48e-1733
neural tube1.77e-1757
neural rod1.77e-1757
future spinal cord1.77e-1757
neural keel1.77e-1757
cerebral hemisphere1.88e-1732
regional part of cerebral cortex6.08e-1722
neocortex1.75e-1520
regional part of brain6.19e-1559
organ6.62e-15511
pre-chordal neural plate5.02e-1461
cerebral cortex1.52e-1325
pallium1.52e-1325
subdivision of digestive tract2.17e-13129
endodermal part of digestive tract2.17e-13129
central nervous system2.30e-1382
brain2.45e-1369
future brain2.45e-1369
endoderm-derived structure5.00e-13169
endoderm5.00e-13169
presumptive endoderm5.00e-13169
neurectoderm6.65e-1390
neural plate2.26e-1286
presumptive neural plate2.26e-1286
regional part of nervous system5.89e-1294
nervous system5.89e-1294
embryonic structure1.27e-11605
developing anatomical structure1.27e-11605
digestive system1.31e-11155
digestive tract1.31e-11155
primitive gut1.31e-11155
germ layer2.62e-11604
embryonic tissue2.62e-11604
presumptive structure2.62e-11604
epiblast (generic)2.62e-11604
embryo2.90e-11612
anatomical system9.75e-11625
anatomical group1.40e-10626
multi-cellular organism1.57e-10659
organ part5.45e-10219
multi-tissue structure6.08e-10347
gastrointestinal system7.77e-1035
intestine8.78e-1027
mixed endoderm/mesoderm-derived structure1.59e-09130
foregut3.05e-0998
anterior region of body5.62e-08129
craniocervical region5.62e-08129
larynx1.78e-079
head1.96e-07123
small intestine3.46e-0714
temporal lobe5.76e-077
upper respiratory tract9.89e-0719
Disease
Ontology termp-valuen
carcinoma7.15e-10106
adenocarcinoma5.13e-0825


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.

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