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Coexpression cluster:C2345: Difference between revisions

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|tf_chipseq_enrich=ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248476596637784
|tf_chipseq_enrich=ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248476596637784
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}}
}}

Revision as of 15:26, 26 November 2012


Full id: C2345_optic_Neural_parietal_spinal_Myoblast_locus_globus



Phase1 CAGE Peaks

Hg19::chr15:68870949..68871019,+p3@CORO2B
Hg19::chr15:68871309..68871354,+p2@CORO2B
Hg19::chr15:68871361..68871409,+p1@CORO2B
Hg19::chr2:105470714..105470723,+p8@POU3F3


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
central nervous system9.22e-3381
nervous system6.34e-3289
neural plate9.29e-3282
presumptive neural plate9.29e-3282
structure with developmental contribution from neural crest1.22e-31132
cell layer1.56e-31309
epithelium2.04e-30306
neural tube6.15e-3056
neural rod6.15e-3056
future spinal cord6.15e-3056
neural keel6.15e-3056
brain1.01e-2868
future brain1.01e-2868
neurectoderm1.03e-2886
regional part of nervous system2.99e-2853
regional part of brain2.99e-2853
tube9.50e-27192
anatomical cluster1.45e-26373
ecto-epithelium1.31e-24104
multi-tissue structure6.57e-24342
anatomical conduit8.68e-24240
pre-chordal neural plate1.84e-2261
regional part of forebrain3.25e-2141
forebrain3.25e-2141
anterior neural tube3.25e-2141
future forebrain3.25e-2141
ectoderm-derived structure4.31e-20171
ectoderm4.31e-20171
presumptive ectoderm4.31e-20171
telencephalon4.88e-2034
brain grey matter6.61e-2034
gray matter6.61e-2034
cerebral hemisphere9.53e-1932
adult organism9.73e-19114
regional part of telencephalon9.77e-1932
anatomical system2.58e-16624
anatomical group5.38e-16625
paraxial mesoderm3.27e-1572
presumptive paraxial mesoderm3.27e-1572
dense mesenchyme tissue3.57e-1573
multi-cellular organism4.75e-15656
cerebral cortex7.61e-1525
pallium7.61e-1525
somite1.02e-1471
presomitic mesoderm1.02e-1471
presumptive segmental plate1.02e-1471
dermomyotome1.02e-1471
trunk paraxial mesoderm1.02e-1471
epithelial vesicle2.47e-1478
skeletal muscle tissue2.89e-1462
striated muscle tissue2.89e-1462
myotome2.89e-1462
muscle tissue5.90e-1464
musculature5.90e-1464
musculature of body5.90e-1464
regional part of cerebral cortex1.68e-1322
neocortex1.84e-1220
embryo2.40e-12592
developing anatomical structure1.10e-11581
multilaminar epithelium1.76e-1183
organ system subdivision4.33e-11223
vasculature2.57e-1078
vascular system2.57e-1078
embryonic structure3.81e-10564
mesenchyme5.58e-10160
entire embryonic mesenchyme5.58e-10160
posterior neural tube7.34e-1015
chordal neural plate7.34e-1015
germ layer7.75e-10560
germ layer / neural crest7.75e-10560
embryonic tissue7.75e-10560
presumptive structure7.75e-10560
germ layer / neural crest derived structure7.75e-10560
epiblast (generic)7.75e-10560
organ part1.22e-09218
artery1.36e-0942
arterial blood vessel1.36e-0942
arterial system1.36e-0942
splanchnic layer of lateral plate mesoderm2.59e-0983
trunk mesenchyme3.50e-09122
segmental subdivision of nervous system5.59e-0913
epithelial tube open at both ends1.37e-0859
blood vessel1.37e-0859
blood vasculature1.37e-0859
vascular cord1.37e-0859
systemic artery1.62e-0833
systemic arterial system1.62e-0833


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
ZNF263#1012748.221841637010680.0002187871180958320.00248476596637784



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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