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Coexpression cluster:C3997: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!3.93e-28!89;UBERON:0001017!4.45e-28!81;UBERON:0002780!3.28e-23!41;UBERON:0001890!3.28e-23!41;UBERON:0003080!3.28e-23!41;UBERON:0006240!3.28e-23!41;UBERON:0000955!4.72e-22!68;UBERON:0006238!4.72e-22!68;UBERON:0001049!6.77e-22!56;UBERON:0005068!6.77e-22!56;UBERON:0006241!6.77e-22!56;UBERON:0007135!6.77e-22!56;UBERON:0000073!2.78e-21!53;UBERON:0002616!2.78e-21!53;UBERON:0001893!1.17e-20!34;UBERON:0001869!1.44e-20!32;UBERON:0003528!1.96e-20!34;UBERON:0002020!1.96e-20!34;UBERON:0004121!3.82e-20!171;UBERON:0000924!3.82e-20!171;UBERON:0006601!3.82e-20!171;UBERON:0003056!5.28e-20!61;UBERON:0003075!5.31e-20!82;UBERON:0007284!5.31e-20!82;UBERON:0002791!7.00e-20!32;UBERON:0002346!4.24e-19!86;UBERON:0007023!3.00e-18!114;UBERON:0010314!2.20e-17!132;UBERON:0011216!3.74e-17!223;UBERON:0000956!2.36e-16!25;UBERON:0000203!2.36e-16!25;UBERON:0010371!3.04e-16!104;UBERON:0002619!6.57e-16!22;UBERON:0001950!1.95e-14!20;UBERON:0000477!2.91e-08!373;UBERON:0000481!4.82e-08!342;UBERON:0000468!5.25e-08!656
|ontology_enrichment_uberon=UBERON:0001016!3.93e-28!89;UBERON:0001017!4.45e-28!81;UBERON:0002780!3.28e-23!41;UBERON:0001890!3.28e-23!41;UBERON:0003080!3.28e-23!41;UBERON:0006240!3.28e-23!41;UBERON:0000955!4.72e-22!68;UBERON:0006238!4.72e-22!68;UBERON:0001049!6.77e-22!56;UBERON:0005068!6.77e-22!56;UBERON:0006241!6.77e-22!56;UBERON:0007135!6.77e-22!56;UBERON:0000073!2.78e-21!53;UBERON:0002616!2.78e-21!53;UBERON:0001893!1.17e-20!34;UBERON:0001869!1.44e-20!32;UBERON:0003528!1.96e-20!34;UBERON:0002020!1.96e-20!34;UBERON:0004121!3.82e-20!171;UBERON:0000924!3.82e-20!171;UBERON:0006601!3.82e-20!171;UBERON:0003056!5.28e-20!61;UBERON:0003075!5.31e-20!82;UBERON:0007284!5.31e-20!82;UBERON:0002791!7.00e-20!32;UBERON:0002346!4.24e-19!86;UBERON:0007023!3.00e-18!114;UBERON:0010314!2.20e-17!132;UBERON:0011216!3.74e-17!223;UBERON:0000956!2.36e-16!25;UBERON:0000203!2.36e-16!25;UBERON:0010371!3.04e-16!104;UBERON:0002619!6.57e-16!22;UBERON:0001950!1.95e-14!20;UBERON:0000477!2.91e-08!373;UBERON:0000481!4.82e-08!342;UBERON:0000468!5.25e-08!656
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}}
}}

Revision as of 16:29, 26 November 2012


Full id: C3997_pineal_merkel_carcinosarcoma_Neural_neuroblastoma_Mesenchymal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:77333117..77333139,+p2@ST6GALNAC5
Hg19::chr1:77333155..77333184,+p1@ST6GALNAC5
Hg19::chr1:77337366..77337379,+p@chr1:77337366..77337379
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
skin fibroblast6.86e-0823
neural cell7.59e-0725
Uber Anatomy
Ontology termp-valuen
nervous system3.93e-2889
central nervous system4.45e-2881
regional part of forebrain3.28e-2341
forebrain3.28e-2341
anterior neural tube3.28e-2341
future forebrain3.28e-2341
brain4.72e-2268
future brain4.72e-2268
neural tube6.77e-2256
neural rod6.77e-2256
future spinal cord6.77e-2256
neural keel6.77e-2256
regional part of nervous system2.78e-2153
regional part of brain2.78e-2153
telencephalon1.17e-2034
cerebral hemisphere1.44e-2032
brain grey matter1.96e-2034
gray matter1.96e-2034
ectoderm-derived structure3.82e-20171
ectoderm3.82e-20171
presumptive ectoderm3.82e-20171
pre-chordal neural plate5.28e-2061
neural plate5.31e-2082
presumptive neural plate5.31e-2082
regional part of telencephalon7.00e-2032
neurectoderm4.24e-1986
adult organism3.00e-18114
structure with developmental contribution from neural crest2.20e-17132
organ system subdivision3.74e-17223
cerebral cortex2.36e-1625
pallium2.36e-1625
ecto-epithelium3.04e-16104
regional part of cerebral cortex6.57e-1622
neocortex1.95e-1420
anatomical cluster2.91e-08373
multi-tissue structure4.82e-08342
multi-cellular organism5.25e-08656
Disease
Ontology termp-valuen
ovarian cancer5.10e-0914


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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