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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1742_teratocarcinoma_H9_hepatoblastoma_pancreatic_choriocarcinoma_pineal_mesodermal
|full_id=C1742_teratocarcinoma_H9_hepatoblastoma_pancreatic_choriocarcinoma_pineal_mesodermal
|id=C1742
|id=C1742

Revision as of 14:20, 12 September 2012


Full id: C1742_teratocarcinoma_H9_hepatoblastoma_pancreatic_choriocarcinoma_pineal_mesodermal



Phase1 CAGE Peaks

Hg19::chr15:55906703..55906714,-p4@PRTG
Hg19::chr15:56035257..56035355,-p1@PRTG
Hg19::chr15:56035356..56035367,-p2@PRTG
Hg19::chr15:56035379..56035390,-p6@PRTG
Hg19::chr15:56035422..56035433,-p5@PRTG


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>

Cell Type
Ontology termp-valuen
epithelial cell1.20e-09254
glial cell (sensu Vertebrata)5.39e-0715
glial cell5.39e-0715
glioblast5.39e-0715
glioblast (sensu Vertebrata)5.39e-0715
Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.83e-17347
anatomical cluster4.09e-14286
cell layer1.11e-13312
epithelium4.00e-13309
regional part of nervous system8.41e-1394
nervous system8.41e-1394
organ part1.04e-12219
multi-cellular organism1.20e-12659
embryo2.00e-12612
central nervous system2.02e-1182
trunk region element5.36e-11107
tube6.71e-11194
organ7.89e-11511
anatomical conduit8.87e-11241
anatomical system1.83e-10625
anatomical group3.10e-10626
organism subdivision4.59e-10365
neural plate6.10e-1086
presumptive neural plate6.10e-1086
embryonic structure7.71e-10605
developing anatomical structure7.71e-10605
germ layer1.54e-09604
embryonic tissue1.54e-09604
presumptive structure1.54e-09604
epiblast (generic)1.54e-09604
brain1.96e-0969
future brain1.96e-0969
ectoderm-derived structure1.94e-08169
cavitated compound organ2.77e-0832
neurectoderm3.03e-0890
primordium5.05e-08168
mesenchyme1.07e-07238
entire embryonic mesenchyme1.07e-07238
neural tube1.57e-0757
neural rod1.57e-0757
future spinal cord1.57e-0757
neural keel1.57e-0757
immaterial anatomical entity2.28e-07126
ectoderm2.35e-07173
presumptive ectoderm2.35e-07173
digestive system5.04e-07155
digestive tract5.04e-07155
primitive gut5.04e-07155
regional part of brain5.36e-0759
abdomen element5.38e-0755
abdominal segment element5.38e-0755
kidney6.21e-0727
kidney mesenchyme6.21e-0727
kidney rudiment6.21e-0727
kidney field6.21e-0727
head6.35e-07123
Disease
Ontology termp-valuen
cell type cancer1.68e-13143
carcinoma1.07e-11106


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
BRCA1#672416.1473845145792.89130901545765e-050.00060501988031533
CHD2#110648.275218267293490.0004028373567101730.00387759729930449
EGR1#195843.990543275848110.0067800983001440.0287637779823194
EP300#203345.419153380978560.00209386927943890.0121153248573584
RAD21#588548.284027116365060.0004011622639122450.00386574881719238
REST#597847.720022972902420.0005286363773650570.00457227781495894
RXRA#6256416.05969371130662.95432243260421e-050.000615492680109217
YY1#752843.928936599883080.007193866269917620.0298391595918792
ZBTB33#10009425.33178002398494.84316058023886e-060.000150004403273893



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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