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Coexpression cluster:C4424: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 20:00, 8 August 2012


Full id: C4424_somatostatinoma_pineal_neuroectodermal_retina_thyroid_Mesenchymal_left



Phase1 CAGE Peaks

Hg19::chr4:75858290..75858299,+p3@PARM1
Hg19::chr4:75858318..75858339,+p1@PARM1
Hg19::chr4:75858349..75858360,+p2@PARM1


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
adult organism1.22e-46115
neural tube7.84e-1957
neural rod7.84e-1957
future spinal cord7.84e-1957
neural keel7.84e-1957
neurectoderm2.60e-1790
regional part of nervous system8.57e-1794
nervous system8.57e-1794
central nervous system3.20e-1682
anterior neural tube3.41e-1642
neural plate4.83e-1686
presumptive neural plate4.83e-1686
regional part of forebrain1.15e-1541
forebrain1.15e-1541
future forebrain1.15e-1541
regional part of brain2.14e-1559
brain2.82e-1369
future brain2.82e-1369
pre-chordal neural plate1.35e-1261
gray matter1.57e-1234
brain grey matter1.57e-1234
telencephalon1.72e-1234
cerebral hemisphere3.39e-1232
regional part of telencephalon5.41e-1233
regional part of cerebral cortex2.16e-1122
neocortex8.11e-1120
ectoderm4.23e-10173
presumptive ectoderm4.23e-10173
embryo6.62e-10612
multi-cellular organism8.59e-10659
cerebral cortex2.53e-0925
pallium2.53e-0925
ectoderm-derived structure3.35e-09169
anterior region of body3.75e-09129
craniocervical region3.75e-09129
multi-tissue structure4.88e-09347
head1.04e-08123
embryonic structure1.51e-08605
developing anatomical structure1.51e-08605
germ layer2.86e-08604
embryonic tissue2.86e-08604
presumptive structure2.86e-08604
epiblast (generic)2.86e-08604
anatomical conduit9.28e-08241
tube2.21e-07194
organism subdivision2.88e-07365


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)

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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

No analysis results for this cluster

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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