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Coexpression cluster:C2834: Difference between revisions

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|tf_chipseq_enrich=REST#5978;4:9.65002871612802:0.000115282561421917:0.0015744730524838
|tf_chipseq_enrich=REST#5978;4:9.65002871612802:0.000115282561421917:0.0015744730524838
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}}
}}

Revision as of 15:45, 26 November 2012


Full id: C2834_nonsmall_argyrophil_pineal_somatostatinoma_occipital_Chondrocyte_peripheral



Phase1 CAGE Peaks

Hg19::chr5:95768869..95768880,-p5@PCSK1
Hg19::chr5:95768891..95768907,-p3@PCSK1
Hg19::chr5:95768919..95768964,-p1@PCSK1
Hg19::chr5:95768973..95768987,-p2@PCSK1


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
neuronal stem cell2.85e-088
GAG secreting cell7.33e-079
carbohydrate secreting cell7.33e-079
Uber Anatomy
Ontology termp-valuen
central nervous system1.93e-4381
nervous system1.75e-4189
neural tube7.04e-3856
neural rod7.04e-3856
future spinal cord7.04e-3856
neural keel7.04e-3856
regional part of nervous system1.36e-3553
regional part of brain1.36e-3553
regional part of forebrain5.19e-3541
forebrain5.19e-3541
anterior neural tube5.19e-3541
future forebrain5.19e-3541
brain2.54e-3268
future brain2.54e-3268
neurectoderm5.54e-3186
neural plate1.01e-2882
presumptive neural plate1.01e-2882
pre-chordal neural plate2.99e-2861
brain grey matter4.74e-2834
gray matter4.74e-2834
telencephalon7.96e-2834
cerebral hemisphere7.82e-2732
regional part of telencephalon4.12e-2632
adult organism1.37e-25114
regional part of cerebral cortex4.72e-2322
ecto-epithelium5.15e-22104
ectoderm-derived structure7.26e-22171
ectoderm7.26e-22171
presumptive ectoderm7.26e-22171
neocortex1.30e-2120
cerebral cortex4.18e-2125
pallium4.18e-2125
structure with developmental contribution from neural crest1.03e-15132
organ system subdivision1.99e-14223
diencephalon1.21e-087
future diencephalon1.21e-087
gyrus1.49e-086
neural nucleus2.34e-089
nucleus of brain2.34e-089
basal ganglion2.93e-089
nuclear complex of neuraxis2.93e-089
aggregate regional part of brain2.93e-089
collection of basal ganglia2.93e-089
cerebral subcortex2.93e-089
anatomical cluster2.09e-07373
multi-cellular organism4.74e-07656
parietal lobe5.47e-075
brainstem6.80e-076
occipital lobe8.99e-075


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
REST#597849.650028716128020.0001152825614219170.0015744730524838



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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