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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1686_anaplastic_clear_gastrointestinal_carcinoid_acute_occipital_neuroectodermal
|full_id=C1686_anaplastic_clear_gastrointestinal_carcinoid_acute_occipital_neuroectodermal
|id=C1686
|id=C1686

Revision as of 14:16, 12 September 2012


Full id: C1686_anaplastic_clear_gastrointestinal_carcinoid_acute_occipital_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr12:72665510..72665534,+p@chr12:72665510..72665534
+
Hg19::chr12:72666523..72666550,+p6@TRHDE
Hg19::chr12:72666612..72666629,+p8@TRHDE
Hg19::chr12:72666647..72666674,+p4@TRHDE
Hg19::chr12:72666686..72666699,+p12@TRHDE


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
regional part of nervous system1.86e-1794
nervous system1.86e-1794
neurectoderm5.16e-1790
organism subdivision1.24e-16365
telencephalon1.72e-1634
cerebral hemisphere3.09e-1632
regional part of telencephalon9.53e-1633
central nervous system9.76e-1682
neural plate1.28e-1586
presumptive neural plate1.28e-1586
neural tube1.31e-1557
neural rod1.31e-1557
future spinal cord1.31e-1557
neural keel1.31e-1557
gray matter1.32e-1534
brain grey matter1.32e-1534
cerebral cortex2.90e-1525
pallium2.90e-1525
brain7.28e-1569
future brain7.28e-1569
pre-chordal neural plate8.25e-1561
adult organism1.70e-14115
regional part of brain1.87e-1459
regional part of cerebral cortex2.13e-1422
anterior neural tube3.24e-1442
regional part of forebrain5.86e-1441
forebrain5.86e-1441
future forebrain5.86e-1441
neocortex1.78e-1320
ectoderm6.99e-13173
presumptive ectoderm6.99e-13173
head2.41e-12123
anterior region of body5.86e-12129
craniocervical region5.86e-12129
ectoderm-derived structure8.68e-12169
multi-tissue structure2.52e-11347
multi-cellular organism3.07e-09659
organ part8.39e-09219


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#1066455.360256373075030.0002259278299937090.00249584055814607



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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