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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2127_parietal_acute_occipital_thyroid_glioblastoma_transitionalcell_putamen
|full_id=C2127_parietal_acute_occipital_thyroid_glioblastoma_transitionalcell_putamen
|id=C2127
|id=C2127

Revision as of 14:48, 12 September 2012


Full id: C2127_parietal_acute_occipital_thyroid_glioblastoma_transitionalcell_putamen



Phase1 CAGE Peaks

Hg19::chr11:30607819..30607867,-p2@MPPED2
Hg19::chr11:30607871..30607882,-p6@MPPED2
Hg19::chr11:30607891..30607935,-p1@MPPED2
Hg19::chr11:30608144..30608178,-p4@MPPED2


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 organism4.67e-46115
central nervous system2.62e-3282
neural tube4.86e-3157
neural rod4.86e-3157
future spinal cord4.86e-3157
neural keel4.86e-3157
regional part of nervous system1.14e-2894
nervous system1.14e-2894
regional part of brain4.54e-2659
brain1.42e-2469
future brain1.42e-2469
anterior neural tube1.76e-2442
regional part of forebrain3.39e-2441
forebrain3.39e-2441
future forebrain3.39e-2441
neural plate2.11e-2386
presumptive neural plate2.11e-2386
neurectoderm1.60e-2190
telencephalon2.76e-2134
gray matter2.88e-2134
brain grey matter2.88e-2134
cerebral hemisphere9.91e-2132
regional part of telencephalon1.26e-2033
ectoderm-derived structure3.06e-18169
anterior region of body9.68e-18129
craniocervical region9.68e-18129
ectoderm2.94e-17173
presumptive ectoderm2.94e-17173
pre-chordal neural plate5.08e-1761
head8.48e-17123
cerebral cortex6.44e-1625
pallium6.44e-1625
regional part of cerebral cortex2.00e-1422
neocortex2.22e-1320
posterior neural tube9.83e-0815
chordal neural plate9.83e-0815
segmental subdivision of nervous system8.24e-0713
nucleus of brain8.30e-079
neural nucleus8.30e-079


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
RAD21#5885410.35503389545638.6948481184721e-050.00129098840296433
TAF1#687243.343046285745290.008005664898701650.0321232379113071
ZNF263#1012748.221841637010680.0002187871180958320.00248098890627694



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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