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Coexpression cluster:C2834

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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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
central nervous system1.21e-3482
regional part of nervous system4.33e-3394
nervous system4.33e-3394
neural tube7.62e-3357
neural rod7.62e-3357
future spinal cord7.62e-3357
neural keel7.62e-3357
adult organism8.12e-30115
regional part of forebrain3.95e-2941
forebrain3.95e-2941
future forebrain3.95e-2941
anterior neural tube5.29e-2842
regional part of brain2.30e-2659
brain4.97e-2669
future brain4.97e-2669
neurectoderm8.28e-2690
neural plate2.78e-2486
presumptive neural plate2.78e-2486
gray matter1.12e-2334
brain grey matter1.12e-2334
telencephalon1.20e-2334
cerebral hemisphere6.08e-2332
regional part of telencephalon9.82e-2333
pre-chordal neural plate2.21e-2061
cerebral cortex1.28e-1825
pallium1.28e-1825
regional part of cerebral cortex1.68e-1822
neocortex2.81e-1720
ectoderm2.41e-15173
presumptive ectoderm2.41e-15173
ectoderm-derived structure3.53e-14169
head1.78e-11123
anterior region of body8.42e-11129
craniocervical region8.42e-11129
multi-cellular organism1.10e-07659
tube3.47e-07194
temporal lobe3.74e-077
diencephalon6.54e-077
future diencephalon6.54e-077


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.