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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1943_extraskeletal_temporal_occipital_adrenal_parietal_duodenum_bone
|full_id=C1943_extraskeletal_temporal_occipital_adrenal_parietal_duodenum_bone
|id=C1943
|id=C1943

Revision as of 14:35, 12 September 2012


Full id: C1943_extraskeletal_temporal_occipital_adrenal_parietal_duodenum_bone



Phase1 CAGE Peaks

Hg19::chr4:66460864..66460869,-p@chr4:66460864..66460869
-
Hg19::chr4:66536057..66536071,-p5@EPHA5
Hg19::chr4:66536169..66536189,-p1@EPHA5
Hg19::chr4:66536196..66536216,-p2@EPHA5
Hg19::chr4:66536221..66536236,-p4@EPHA5


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
regional part of nervous system7.97e-3494
nervous system7.97e-3494
central nervous system2.19e-3282
neural plate1.01e-3186
presumptive neural plate1.01e-3186
neural tube2.08e-3057
neural rod2.08e-3057
future spinal cord2.08e-3057
neural keel2.08e-3057
neurectoderm2.83e-3090
brain5.03e-2769
future brain5.03e-2769
regional part of brain8.91e-2759
ectoderm-derived structure1.10e-25169
ectoderm4.45e-25173
presumptive ectoderm4.45e-25173
regional part of forebrain3.36e-2341
forebrain3.36e-2341
future forebrain3.36e-2341
anterior neural tube4.72e-2342
pre-chordal neural plate1.56e-2161
head3.36e-21123
anterior region of body3.39e-20129
craniocervical region3.39e-20129
gray matter4.64e-2034
brain grey matter4.64e-2034
tube5.25e-20194
telencephalon8.46e-2034
cerebral hemisphere2.05e-1932
regional part of telencephalon3.24e-1933
epithelium7.07e-19309
cell layer1.73e-18312
organism subdivision2.94e-17365
multi-tissue structure2.02e-16347
cerebral cortex2.35e-1625
pallium2.35e-1625
regional part of cerebral cortex1.09e-1522
anatomical conduit1.15e-15241
adult organism1.64e-15115
anatomical cluster4.14e-15286
neocortex2.25e-1420
embryo1.95e-11612
embryonic structure2.56e-11605
developing anatomical structure2.56e-11605
germ layer4.51e-11604
embryonic tissue4.51e-11604
presumptive structure4.51e-11604
epiblast (generic)4.51e-11604
multi-cellular organism2.11e-09659
organ part5.15e-09219
anatomical system1.34e-08625
posterior neural tube1.85e-0815
chordal neural plate1.85e-0815
artery1.88e-0842
arterial blood vessel1.88e-0842
arterial system1.88e-0842
anatomical group1.98e-08626
systemic artery6.15e-0833
systemic arterial system6.15e-0833
skeletal muscle tissue2.53e-0761
striated muscle tissue2.53e-0761
myotome2.53e-0761
muscle tissue2.58e-0763
musculature2.58e-0763
musculature of body2.58e-0763
somite4.13e-0783
paraxial mesoderm4.13e-0783
presomitic mesoderm4.13e-0783
presumptive segmental plate4.13e-0783
trunk paraxial mesoderm4.13e-0783
presumptive paraxial mesoderm4.13e-0783
splanchnic layer of lateral plate mesoderm6.01e-0784


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
CTCF#1066444.288205098460020.005152015588243280.0239440795665957
E2F1#186943.925911371903460.007214984547106360.0298816580527121
E2F6#187644.013724585357910.006632118233933880.0283038491432584
FOS#235347.198364247115530.0006947858453382510.00559854478059421
RAD21#588548.284027116365060.0004011622639122450.00386931895832388
TRIM28#10155414.872420036214.00368496902357e-050.000734869691528739
ZNF263#1012746.577473309608540.0009875103237900160.00709462686292258



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.