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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3997_pineal_merkel_carcinosarcoma_Neural_neuroblastoma_Mesenchymal_mesenchymal
|full_id=C3997_pineal_merkel_carcinosarcoma_Neural_neuroblastoma_Mesenchymal_mesenchymal
|id=C3997
|id=C3997

Revision as of 17:00, 12 September 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
non-terminally differentiated cell2.17e-08180
neurectodermal cell1.91e-0759
neural cell3.08e-0725
skin fibroblast5.70e-0723
Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.11e-2994
nervous system3.11e-2994
central nervous system4.90e-2882
ectoderm-derived structure2.82e-23169
anterior neural tube6.69e-2342
neural tube1.31e-2257
neural rod1.31e-2257
future spinal cord1.31e-2257
neural keel1.31e-2257
regional part of forebrain1.42e-2241
forebrain1.42e-2241
future forebrain1.42e-2241
ectoderm1.51e-22173
presumptive ectoderm1.51e-22173
brain1.84e-2269
future brain1.84e-2269
neural plate6.35e-2286
presumptive neural plate6.35e-2286
neurectoderm1.10e-2090
adult organism1.23e-20115
regional part of brain2.50e-2059
pre-chordal neural plate6.51e-2061
telencephalon1.19e-1934
cerebral hemisphere1.39e-1932
gray matter1.54e-1934
brain grey matter1.54e-1934
regional part of telencephalon4.49e-1933
anterior region of body8.80e-19129
craniocervical region8.80e-19129
head1.04e-18123
organism subdivision3.96e-18365
cerebral cortex8.26e-1625
pallium8.26e-1625
regional part of cerebral cortex3.17e-1522
neocortex8.25e-1420
multi-cellular organism1.57e-09659
multi-tissue structure1.87e-09347
organ part1.05e-07219
epithelium3.73e-07309
cell layer7.73e-07312
anatomical system9.35e-07625
Disease
Ontology termp-valuen
ovarian cancer8.70e-0814


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

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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