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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2893_Fibroblast_Olfactory_heart_papillary_left_basal_glioblastoma
|full_id=C2893_Fibroblast_Olfactory_heart_papillary_left_basal_glioblastoma
|id=C2893
|id=C2893

Revision as of 15:41, 12 September 2012


Full id: C2893_Fibroblast_Olfactory_heart_papillary_left_basal_glioblastoma



Phase1 CAGE Peaks

Hg19::chr7:32110008..32110058,-p4@PDE1C
Hg19::chr7:32110421..32110445,-p3@PDE1C
Hg19::chr7:32110451..32110523,-p1@PDE1C
Hg19::chr7:32111009..32111055,-p5@PDE1C


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><br>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell2.12e-12180
Uber Anatomy
Ontology termp-valuen
neural tube2.90e-2857
neural rod2.90e-2857
future spinal cord2.90e-2857
neural keel2.90e-2857
adult organism3.29e-27115
central nervous system5.58e-2782
brain4.68e-2569
future brain4.68e-2569
regional part of nervous system6.80e-2594
nervous system6.80e-2594
regional part of brain1.82e-2459
neural plate3.80e-2186
presumptive neural plate3.80e-2186
regional part of forebrain4.32e-2141
forebrain4.32e-2141
future forebrain4.32e-2141
anterior neural tube5.24e-2142
neurectoderm4.20e-2090
gray matter1.07e-1934
brain grey matter1.07e-1934
telencephalon1.18e-1934
regional part of telencephalon4.22e-1933
cerebral hemisphere3.60e-1832
ectoderm-derived structure7.16e-16169
ectoderm1.94e-15173
presumptive ectoderm1.94e-15173
organism subdivision2.15e-15365
pre-chordal neural plate7.06e-1561
head1.39e-14123
tube1.44e-14194
anterior region of body1.90e-14129
craniocervical region1.90e-14129
cerebral cortex2.87e-1425
pallium2.87e-1425
anatomical conduit2.95e-14241
anatomical cluster4.02e-14286
regional part of cerebral cortex1.51e-1222
epithelium3.00e-12309
cell layer8.05e-12312
neocortex1.70e-1120
multi-cellular organism8.03e-10659
multi-tissue structure2.86e-09347
organ part9.39e-09219
posterior neural tube2.19e-0815
chordal neural plate2.19e-0815
anatomical system1.31e-07625
segmental subdivision of nervous system1.54e-0713
anatomical group1.81e-07626
nucleus of brain6.27e-079
neural nucleus6.27e-079
segmental subdivision of hindbrain7.32e-0712
hindbrain7.32e-0712
presumptive hindbrain7.32e-0712


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
CTBP2#1488231.35850016966410.001492676882047230.00954412151855826
SUZ12#23512225.05789045553150.002325256716520610.0131874822816561



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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