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Coexpression cluster:C2945: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820729383035805!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435747645454396
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820729383035805!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435747645454396
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}}
}}

Revision as of 15:49, 26 November 2012


Full id: C2945_seminal_extraskeletal_leiomyoblastoma_thyroid_spinal_serous_ductus



Phase1 CAGE Peaks

Hg19::chr9:4299959..4299974,-p4@GLIS3
Hg19::chr9:4299979..4299996,-p3@GLIS3
Hg19::chr9:4300016..4300039,-p2@GLIS3
Hg19::chr9:4300050..4300118,-p1@GLIS3


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
contractile cell3.04e-0859
muscle cell8.91e-0855
muscle precursor cell9.92e-0858
myoblast9.92e-0858
multi-potent skeletal muscle stem cell9.92e-0858
non-terminally differentiated cell2.02e-07106
fibroblast6.75e-0776
Uber Anatomy
Ontology termp-valuen
multi-cellular organism4.86e-23656
anatomical system5.88e-23624
anatomical group1.31e-22625
organ3.14e-21503
multi-tissue structure1.33e-18342
tube1.28e-17192
anatomical cluster1.66e-17373
anatomical conduit1.75e-17240
developing anatomical structure3.05e-16581
embryo3.32e-16592
cell layer5.29e-16309
epithelium5.47e-16306
mesenchyme5.09e-15160
entire embryonic mesenchyme5.09e-15160
germ layer4.63e-13560
germ layer / neural crest4.63e-13560
embryonic tissue4.63e-13560
presumptive structure4.63e-13560
germ layer / neural crest derived structure4.63e-13560
epiblast (generic)4.63e-13560
embryonic structure8.47e-13564
structure with developmental contribution from neural crest1.02e-12132
brain4.46e-1268
future brain4.46e-1268
neural tube5.06e-1256
neural rod5.06e-1256
future spinal cord5.06e-1256
neural keel5.06e-1256
central nervous system5.59e-1281
neural plate1.97e-1182
presumptive neural plate1.97e-1182
trunk mesenchyme1.15e-10122
regional part of nervous system1.27e-1053
regional part of brain1.27e-1053
trunk2.13e-10199
neurectoderm1.08e-0986
nervous system1.64e-0989
organism subdivision1.10e-08264
epithelial tube1.92e-08117
regional part of forebrain2.44e-0841
forebrain2.44e-0841
anterior neural tube2.44e-0841
future forebrain2.44e-0841
adult organism2.77e-08114
brain grey matter4.44e-0834
gray matter4.44e-0834
epithelial vesicle1.39e-0778
telencephalon1.71e-0734
compound organ1.92e-0768
paraxial mesoderm2.33e-0772
presumptive paraxial mesoderm2.33e-0772
mesoderm2.57e-07315
mesoderm-derived structure2.57e-07315
presumptive mesoderm2.57e-07315
dense mesenchyme tissue2.57e-0773
pre-chordal neural plate2.63e-0761
regional part of telencephalon2.83e-0732
muscle tissue2.84e-0764
musculature2.84e-0764
musculature of body2.84e-0764
somite2.94e-0771
presomitic mesoderm2.94e-0771
presumptive segmental plate2.94e-0771
dermomyotome2.94e-0771
trunk paraxial mesoderm2.94e-0771
skeletal muscle tissue3.30e-0762
striated muscle tissue3.30e-0762
myotome3.30e-0762
musculoskeletal system4.09e-07167
cavitated compound organ8.16e-0731
organ system subdivision9.00e-07223
cerebral hemisphere9.66e-0732


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#1066445.360256373075030.001211145381643620.00820729383035805
EP300#203346.77394172622320.0004748459821442640.00435747645454396



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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