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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4691_teratocarcinoma_carcinoid_merkel_retinoblastoma_testicular_carcinosarcoma_small
|full_id=C4691_teratocarcinoma_carcinoid_merkel_retinoblastoma_testicular_carcinosarcoma_small
|id=C4691
|id=C4691

Revision as of 17:48, 12 September 2012


Full id: C4691_teratocarcinoma_carcinoid_merkel_retinoblastoma_testicular_carcinosarcoma_small



Phase1 CAGE Peaks

Hg19::chr7:64035038..64035062,+p2@uc003ttc.1
Hg19::chr7:64035065..64035085,+p1@uc003ttc.1
Hg19::chr7:64035097..64035108,+p3@uc003ttc.1


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
epithelial cell of nephron2.24e-0916
kidney cell4.04e-0918
kidney epithelial cell4.04e-0918
kidney tubule cell9.38e-0912
nephron tubule epithelial cell9.38e-0912
kidney cortical cell1.43e-0713
renal cortical epithelial cell1.43e-0713
neural cell2.75e-0725
Uber Anatomy
Ontology termp-valuen
neural plate8.61e-1986
presumptive neural plate8.61e-1986
anterior region of body1.81e-18129
craniocervical region1.81e-18129
head3.08e-18123
ectoderm-derived structure4.43e-18169
neurectoderm2.94e-1790
ectoderm3.83e-17173
presumptive ectoderm3.83e-17173
cell layer1.04e-16312
central nervous system1.89e-1682
pre-chordal neural plate2.14e-1661
regional part of nervous system6.44e-1694
nervous system6.44e-1694
epithelium1.26e-15309
brain7.98e-1569
future brain7.98e-1569
multi-tissue structure1.25e-14347
organism subdivision1.96e-13365
organ part2.30e-13219
regional part of brain3.77e-1359
neural tube1.39e-1257
neural rod1.39e-1257
future spinal cord1.39e-1257
neural keel1.39e-1257
anatomical cluster1.05e-10286
telencephalon6.67e-1034
visual system1.01e-0921
regional part of forebrain1.09e-0941
forebrain1.09e-0941
future forebrain1.09e-0941
regional part of telencephalon1.31e-0933
cerebral hemisphere1.90e-0932
nephron epithelium2.24e-0916
nephron2.24e-0916
uriniferous tubule2.24e-0916
metanephric mesenchyme2.24e-0916
nephrogenic mesenchyme2.24e-0916
gray matter2.40e-0934
brain grey matter2.40e-0934
eye2.44e-0920
sensory system3.46e-0924
entire sense organ system3.46e-0924
anterior neural tube3.55e-0942
camera-type eye4.98e-0919
simple eye4.98e-0919
ocular region4.98e-0919
optic cup4.98e-0919
eye primordium4.98e-0919
optic vesicle4.98e-0919
sense organ8.34e-0923
renal tubule9.38e-0912
nephron tubule9.38e-0912
nephron tubule epithelium9.38e-0912
tube1.20e-08194
excretory tube1.99e-0817
mesonephric epithelium1.99e-0817
mesonephric tubule1.99e-0817
nephric duct1.99e-0817
kidney epithelium1.99e-0817
renal duct1.99e-0817
mesonephric duct1.99e-0817
pronephric duct1.99e-0817
face3.09e-0821
embryonic structure5.04e-08605
developing anatomical structure5.04e-08605
anatomical conduit5.44e-08241
embryo7.68e-08612
germ layer9.48e-08604
embryonic tissue9.48e-08604
presumptive structure9.48e-08604
epiblast (generic)9.48e-08604
anatomical group1.05e-07626
anatomical system1.30e-07625
mesonephros1.34e-0718
pronephros1.34e-0718
nephrogenic cord1.34e-0718
pronephric mesoderm1.34e-0718
rostral part of nephrogenic cord1.34e-0718
presumptive pronephric mesoderm1.34e-0718
cortex of kidney1.43e-0713
renal parenchyma1.43e-0713
organ1.54e-07511
cerebral cortex3.04e-0725
pallium3.04e-0725
parenchyma3.11e-0717
urogenital ridge5.26e-0720
multi-cellular organism5.56e-07659
ectodermal placode6.02e-0729
anterior segment of eyeball8.65e-0714


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
NFYB#4801316.75979325353650.0002123649923296180.00246654664523054



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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