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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C340_hepatocellular_skeletal_breast_putamen_mucinous_pituitary_hepatoblastoma
|full_id=C340_hepatocellular_skeletal_breast_putamen_mucinous_pituitary_hepatoblastoma
|id=C340
|id=C340

Revision as of 16:19, 12 September 2012


Full id: C340_hepatocellular_skeletal_breast_putamen_mucinous_pituitary_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr7:94285674..94285689,+p1@PEG10
Hg19::chr7:94292678..94292708,-p@chr7:94292678..94292708
-
Hg19::chr7:94292685..94292712,+p3@PEG10
Hg19::chr7:94292726..94292754,-p@chr7:94292726..94292754
-
Hg19::chr7:94292734..94292850,+p2@PEG10
Hg19::chr7:94292773..94292786,-p@chr7:94292773..94292786
-
Hg19::chr7:94292829..94292871,-p@chr7:94292829..94292871
-
Hg19::chr7:94293053..94293080,+p1@CU690760
Hg19::chr7:94293245..94293269,+p2@CU690760
Hg19::chr7:94293817..94293830,+p14@PEG10
Hg19::chr7:94293846..94293857,+p27@PEG10
Hg19::chr7:94293862..94293872,+p24@PEG10
Hg19::chr7:94293938..94293949,+p18@PEG10
Hg19::chr7:94294066..94294084,+p13@PEG10
Hg19::chr7:94294134..94294144,+p22@PEG10
Hg19::chr7:94294191..94294215,+p8@PEG10
Hg19::chr7:94294239..94294250,+p25@PEG10
Hg19::chr7:94294286..94294316,+p6@PEG10
Hg19::chr7:94294313..94294347,-p1@CU690761
Hg19::chr7:94294329..94294346,+p16@PEG10
Hg19::chr7:94294370..94294381,-p@chr7:94294370..94294381
-
Hg19::chr7:94294382..94294404,+p11@PEG10
Hg19::chr7:94294389..94294434,-p@chr7:94294389..94294434
-
Hg19::chr7:94294417..94294461,+p1@AB384093
Hg19::chr7:94294477..94294489,+p@chr7:94294477..94294489
+
Hg19::chr7:94294495..94294511,+p@chr7:94294495..94294511
+
Hg19::chr7:94294567..94294582,+p9@PEG10
Hg19::chr7:94294623..94294645,+p4@PEG10
Hg19::chr7:94294932..94294973,-p@chr7:94294932..94294973
-
Hg19::chr7:94294939..94294976,+p7@PEG10
Hg19::chr7:94295525..94295551,+p15@PEG10
Hg19::chr7:94297514..94297599,+p5@PEG10
Hg19::chr7:94298287..94298339,+p@chr7:94298287..94298339
+
Hg19::chr7:94298512..94298534,+p@chr7:94298512..94298534
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
multi-tissue structure4.55e-27347
central nervous system6.72e-2682
regional part of nervous system1.10e-2494
nervous system1.10e-2494
cell layer1.55e-24312
organism subdivision2.21e-24365
epithelium5.13e-24309
neural tube7.18e-2357
neural rod7.18e-2357
future spinal cord7.18e-2357
neural keel7.18e-2357
regional part of brain2.81e-2259
anatomical cluster1.69e-21286
brain2.25e-2169
future brain2.25e-2169
neurectoderm1.88e-2090
ectoderm6.83e-20173
presumptive ectoderm6.83e-20173
neural plate1.31e-1886
presumptive neural plate1.31e-1886
organ part1.59e-18219
ectoderm-derived structure2.74e-18169
tube5.91e-18194
regional part of forebrain6.40e-1741
forebrain6.40e-1741
future forebrain6.40e-1741
anterior neural tube1.70e-1642
anatomical conduit3.47e-16241
anterior region of body2.71e-15129
craniocervical region2.71e-15129
head5.08e-15123
gray matter5.75e-1534
brain grey matter5.75e-1534
pre-chordal neural plate8.01e-1561
telencephalon3.17e-1434
regional part of telencephalon5.28e-1433
cerebral hemisphere7.76e-1432
multi-cellular organism3.29e-13659
embryo3.67e-13612
embryonic structure2.37e-11605
developing anatomical structure2.37e-11605
germ layer3.41e-11604
embryonic tissue3.41e-11604
presumptive structure3.41e-11604
epiblast (generic)3.41e-11604
cerebral cortex9.71e-1125
pallium9.71e-1125
regional part of cerebral cortex2.88e-1022
anatomical group4.13e-10626
anatomical system6.02e-10625
mesenchyme1.50e-09238
entire embryonic mesenchyme1.50e-09238
neocortex3.13e-0920
posterior neural tube1.28e-0715
chordal neural plate1.28e-0715
organ segment1.58e-0797
trunk1.76e-07216
primordium3.28e-07168
organ3.77e-07511
trunk region element6.85e-07107
Disease
Ontology termp-valuen
cell type cancer1.24e-10143
carcinoma4.51e-07106


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

No analysis results for this cluster

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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