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Coexpression cluster:C2809

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Full id: C2809_cerebellum_neuroectodermal_Monocytederived_Macrophage_carcinoid_Neural_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr5:147007238..147007242,-p@chr5:147007238..147007242
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Hg19::chr5:147162202..147162227,-p2@JAKMIP2
Hg19::chr5:147162247..147162262,-p4@JAKMIP2
Hg19::chr5:147162263..147162332,-p1@JAKMIP2


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>


Uber Anatomy
Ontology termp-valuen
nervous system3.27e-3989
central nervous system4.56e-3881
neural tube9.86e-3756
neural rod9.86e-3756
future spinal cord9.86e-3756
neural keel9.86e-3756
regional part of nervous system7.47e-3553
regional part of brain7.47e-3553
neurectoderm6.39e-3286
brain2.38e-3168
future brain2.38e-3168
neural plate2.20e-2982
presumptive neural plate2.20e-2982
regional part of forebrain7.38e-2841
forebrain7.38e-2841
anterior neural tube7.38e-2841
future forebrain7.38e-2841
pre-chordal neural plate4.18e-2461
telencephalon2.53e-2334
brain grey matter2.67e-2334
gray matter2.67e-2334
regional part of telencephalon5.98e-2232
cerebral hemisphere7.08e-2232
ecto-epithelium1.62e-20104
ectoderm-derived structure2.97e-19171
ectoderm2.97e-19171
presumptive ectoderm2.97e-19171
adult organism1.08e-18114
cerebral cortex1.22e-1725
pallium1.22e-1725
regional part of cerebral cortex3.99e-1622
neocortex1.02e-1420
hematopoietic system6.42e-1498
blood island6.42e-1498
organ system subdivision6.61e-14223
structure with developmental contribution from neural crest6.18e-13132
hemolymphoid system2.76e-11108
bone marrow4.59e-1076
posterior neural tube6.97e-1015
chordal neural plate6.97e-1015
bone element2.15e-0982
immune system2.91e-0993
segmental subdivision of nervous system7.89e-0913
skeletal element2.26e-0890
segmental subdivision of hindbrain3.79e-0812
hindbrain3.79e-0812
presumptive hindbrain3.79e-0812
skeletal system3.11e-07100
neural nucleus4.20e-079
nucleus of brain4.20e-079
Disease
Ontology termp-valuen
neuroectodermal tumor2.45e-0710


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
EP300#203335.08045629466740.01144298405398240.0419139975314371
JUND#372735.245997956403270.01043432751748420.0387122817619372
RAD21#588537.766275421592250.0033411193858720.017275269446066
REST#597837.237521537096020.004104697304192610.0195901147809977
ZNF263#1012736.166381227758010.006539814347975980.0279888403347237



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.