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Coexpression cluster:C2593: Difference between revisions

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|tf_chipseq_enrich=USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508291841131114
|tf_chipseq_enrich=USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508291841131114
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}}
}}

Revision as of 15:36, 26 November 2012


Full id: C2593_heart_thyroid_retina_left_umbilical_smooth_pituitary



Phase1 CAGE Peaks

Hg19::chr1:55013889..55013912,+p1@ACOT11
Hg19::chr1:55013918..55013934,+p3@ACOT11
Hg19::chr4:186733169..186733170,-p29@SORBS2
Hg19::chr4:186733332..186733356,-p5@SORBS2


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


GO IDGO nameFDR corrected p-value
GO:0016291acyl-CoA thioesterase activity0.0164969859543486
GO:0016289CoA hydrolase activity0.0164969859543486
GO:0009266response to temperature stimulus0.0164969859543486
GO:0009628response to abiotic stimulus0.0464543083416553
GO:0016790thiolester hydrolase activity0.0464543083416553
GO:0004091carboxylesterase activity0.0464543083416553
GO:0006631fatty acid metabolic process0.0464543083416553



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><br>


Uber Anatomy
Ontology termp-valuen
adult organism6.98e-62114
neural tube2.48e-3956
neural rod2.48e-3956
future spinal cord2.48e-3956
neural keel2.48e-3956
neural plate1.38e-3882
presumptive neural plate1.38e-3882
central nervous system9.19e-3881
brain1.35e-3768
future brain1.35e-3768
regional part of nervous system3.31e-3753
regional part of brain3.31e-3753
nervous system1.39e-3689
neurectoderm1.52e-3686
regional part of forebrain3.25e-3141
forebrain3.25e-3141
anterior neural tube3.25e-3141
future forebrain3.25e-3141
pre-chordal neural plate4.77e-2961
organ system subdivision2.44e-28223
structure with developmental contribution from neural crest4.43e-28132
ecto-epithelium1.21e-27104
ectoderm-derived structure1.89e-25171
ectoderm1.89e-25171
presumptive ectoderm1.89e-25171
telencephalon2.03e-2534
brain grey matter4.10e-2534
gray matter4.10e-2534
cerebral hemisphere3.59e-2432
regional part of telencephalon9.29e-2432
anatomical cluster7.80e-21373
multi-tissue structure1.80e-20342
cerebral cortex2.64e-1825
pallium2.64e-1825
regional part of cerebral cortex1.63e-1722
organ1.46e-16503
neocortex6.25e-1620
embryo6.17e-14592
developing anatomical structure1.83e-13581
germ layer2.18e-13560
germ layer / neural crest2.18e-13560
embryonic tissue2.18e-13560
presumptive structure2.18e-13560
germ layer / neural crest derived structure2.18e-13560
epiblast (generic)2.18e-13560
embryonic structure2.25e-13564
multi-cellular organism7.45e-13656
anatomical system1.04e-11624
tube1.32e-11192
anatomical group1.38e-11625
epithelium3.54e-11306
anatomical conduit3.92e-11240
cell layer4.93e-11309
posterior neural tube3.09e-0915
chordal neural plate3.09e-0915
organ part1.12e-08218
basal ganglion1.51e-089
nuclear complex of neuraxis1.51e-089
aggregate regional part of brain1.51e-089
collection of basal ganglia1.51e-089
cerebral subcortex1.51e-089
neural nucleus2.88e-089
nucleus of brain2.88e-089
segmental subdivision of nervous system8.71e-0813
tissue2.04e-07773
segmental subdivision of hindbrain2.67e-0712
hindbrain2.67e-0712
presumptive hindbrain2.67e-0712
diencephalon3.34e-077
future diencephalon3.34e-077
telencephalic nucleus5.79e-077
gyrus9.34e-076


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
USF1#739146.361499277207960.0006105011399140830.00508291841131114



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.