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Coexpression cluster:C2941

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Full id: C2941_parietal_medulloblastoma_lung_occipital_Neural_temporal_small



Phase1 CAGE Peaks

Hg19::chr9:14313893..14313908,-p7@NFIB
Hg19::chr9:14314066..14314075,-p11@NFIB
Hg19::chr9:14314106..14314119,-p5@NFIB
Hg19::chr9:14314131..14314147,-p2@NFIB


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>


Uber Anatomy
Ontology termp-valuen
anatomical cluster3.42e-42286
anatomical conduit8.72e-40241
epithelium4.01e-36309
cell layer4.07e-36312
tube6.51e-36194
multi-tissue structure1.20e-30347
neurectoderm3.90e-2890
regional part of nervous system1.50e-2794
nervous system1.50e-2794
neural plate2.31e-2786
presumptive neural plate2.31e-2786
ectoderm7.58e-27173
presumptive ectoderm7.58e-27173
ectoderm-derived structure6.07e-26169
central nervous system1.52e-2582
multi-cellular organism3.33e-25659
embryonic structure2.15e-24605
developing anatomical structure2.15e-24605
embryo2.25e-24612
germ layer6.20e-24604
embryonic tissue6.20e-24604
presumptive structure6.20e-24604
epiblast (generic)6.20e-24604
anatomical system1.18e-23625
neural tube1.18e-2357
neural rod1.18e-2357
future spinal cord1.18e-2357
neural keel1.18e-2357
anatomical group2.85e-23626
adult organism1.29e-22115
brain2.25e-2269
future brain2.25e-2269
organism subdivision4.69e-22365
head3.73e-21123
regional part of brain3.81e-2159
anterior region of body1.98e-20129
craniocervical region1.98e-20129
pre-chordal neural plate3.58e-1861
anterior neural tube1.74e-1742
regional part of forebrain4.34e-1741
forebrain4.34e-1741
future forebrain4.34e-1741
telencephalon1.82e-1634
gray matter2.35e-1634
brain grey matter2.35e-1634
regional part of telencephalon3.81e-1633
cerebral hemisphere5.31e-1632
organ part5.60e-16219
cerebral cortex2.62e-1325
pallium2.62e-1325
epithelial tube2.95e-13118
primordium9.52e-13168
vasculature2.90e-1279
vascular system2.90e-1279
splanchnic layer of lateral plate mesoderm4.52e-1284
regional part of cerebral cortex1.18e-1122
vessel6.44e-1169
organ6.85e-11511
neocortex1.56e-1020
circulatory system4.38e-10113
blood vessel6.88e-1060
epithelial tube open at both ends6.88e-1060
blood vasculature6.88e-1060
vascular cord6.88e-1060
cardiovascular system2.26e-09110
compound organ1.37e-0869
endothelium8.04e-0818
blood vessel endothelium8.04e-0818
cardiovascular system endothelium8.04e-0818
mesenchyme1.07e-07238
entire embryonic mesenchyme1.07e-07238
primary circulatory organ1.54e-0727
unilaminar epithelium1.70e-07138
simple squamous epithelium1.81e-0722
posterior neural tube2.22e-0715
chordal neural plate2.22e-0715
squamous epithelium2.75e-0725
organ segment8.66e-0797


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
E2F1#186944.907389214879320.001724022357361790.010688304106643
E2F6#187645.017155731697390.00157802193473060.00999860661538124
MYC#460945.22228187160940.001344309395272740.00890287437748189
REST#597849.650028716128020.0001152825614219170.0015765346906303



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.