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|ontology_enrichment_disease=DOID:305!5.26e-08!106
|ontology_enrichment_disease=DOID:305!5.26e-08!106
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}}

Revision as of 16:57, 8 August 2012


Full id: C1159_Mast_cerebellum_colon_choriocarcinoma_H9_Melanocyte_occipital



Phase1 CAGE Peaks

Hg19::chr12:108523388..108523427,+p2@WSCD2
Hg19::chr12:63327799..63327812,-p7@PPM1H
Hg19::chr12:63328619..63328637,-p4@PPM1H
Hg19::chr12:63328657..63328672,-p3@PPM1H
Hg19::chr12:63328853..63328870,-p2@PPM1H
Hg19::chr12:63328878..63328888,-p5@PPM1H
Hg19::chr12:63328897..63328942,-p1@PPM1H


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


GO IDGO nameFDR corrected p-value
GO:0015071protein phosphatase type 2C activity0.0369564026814861
GO:0008287protein serine/threonine phosphatase complex0.0369564026814861
GO:0004722protein serine/threonine phosphatase activity0.0369564026814861



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 organism1.26e-29115
neural tube1.04e-2557
neural rod1.04e-2557
future spinal cord1.04e-2557
neural keel1.04e-2557
regional part of brain1.89e-2359
central nervous system3.50e-2282
brain1.06e-2069
future brain1.06e-2069
regional part of forebrain5.01e-2041
forebrain5.01e-2041
future forebrain5.01e-2041
anterior neural tube5.82e-2042
regional part of nervous system1.26e-1994
nervous system1.26e-1994
neural plate2.33e-1886
presumptive neural plate2.33e-1886
telencephalon1.17e-1634
gray matter1.67e-1634
brain grey matter1.67e-1634
neurectoderm4.32e-1690
regional part of telencephalon5.08e-1633
cerebral hemisphere2.07e-1532
regional part of cerebral cortex1.48e-1322
pre-chordal neural plate1.63e-1361
neocortex2.06e-1220
cerebral cortex9.68e-1225
pallium9.68e-1225
head2.54e-09123
organ2.83e-09511
anterior region of body2.91e-09129
craniocervical region2.91e-09129
tube4.44e-09194
anatomical cluster2.31e-07286
anatomical conduit4.23e-07241
posterior neural tube5.87e-0715
chordal neural plate5.87e-0715
Disease
Ontology termp-valuen
carcinoma5.26e-08106


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.