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Coexpression cluster:C1667: Difference between revisions

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|tf_chipseq_enrich=BHLHE40#8553;2:17.948725418791:0.00474781285983895:0.022317797608638!HNF4G#3174;2:11.5013690105787:0.0112743830492105:0.0413718875400194!NANOG#79923;2:11.6979113924051:0.0109116495195608:0.0402146151518601
|tf_chipseq_enrich=BHLHE40#8553;2:17.948725418791:0.00474781285983895:0.022317797608638!HNF4G#3174;2:11.5013690105787:0.0112743830492105:0.0413718875400194!NANOG#79923;2:11.6979113924051:0.0109116495195608:0.0402146151518601
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}}
}}

Revision as of 15:02, 26 November 2012


Full id: C1667_corpus_diaphragm_globus_tongue_diencephalon_optic_thalamus



Phase1 CAGE Peaks

Hg19::chr12:21680455..21680478,+p2@C12orf39
Hg19::chr12:21680481..21680499,+p7@C12orf39
Hg19::chr14:35183743..35183754,-p9@CFL2
Hg19::chr14:35183755..35183770,-p7@CFL2
Hg19::chr1:201857798..201857813,+p2@SHISA4


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.91e-29114
structure with developmental contribution from neural crest2.16e-27132
neural tube2.40e-2556
neural rod2.40e-2556
future spinal cord2.40e-2556
neural keel2.40e-2556
neural plate1.41e-2482
presumptive neural plate1.41e-2482
multi-tissue structure6.56e-24342
nervous system1.31e-2389
regional part of nervous system1.32e-2353
regional part of brain1.32e-2353
central nervous system7.25e-2381
brain7.94e-2268
future brain7.94e-2268
neurectoderm1.01e-2186
anatomical cluster2.27e-20373
ectoderm-derived structure7.36e-19171
ectoderm7.36e-19171
presumptive ectoderm7.36e-19171
ecto-epithelium1.20e-18104
regional part of forebrain1.22e-1841
forebrain1.22e-1841
anterior neural tube1.22e-1841
future forebrain1.22e-1841
cell layer5.54e-18309
epithelium9.41e-18306
pre-chordal neural plate1.77e-1661
brain grey matter1.87e-1634
gray matter1.87e-1634
telencephalon1.90e-1634
regional part of telencephalon3.52e-1532
cerebral hemisphere4.20e-1532
anatomical conduit1.99e-14240
organ system subdivision2.61e-14223
tube9.03e-14192
multi-cellular organism5.40e-13656
anatomical system3.32e-12624
anatomical group6.32e-12625
regional part of cerebral cortex1.35e-1122
cerebral cortex6.42e-1125
pallium6.42e-1125
neocortex2.54e-1020
mesenchyme8.76e-09160
entire embryonic mesenchyme8.76e-09160
organ part1.26e-08218
posterior neural tube6.80e-0815
chordal neural plate6.80e-0815
organ7.04e-08503
organism subdivision8.68e-08264
dense mesenchyme tissue1.08e-0773
embryo1.55e-07592
paraxial mesoderm2.11e-0772
presumptive paraxial mesoderm2.11e-0772
neural nucleus2.81e-079
nucleus of brain2.81e-079
basal ganglion3.69e-079
nuclear complex of neuraxis3.69e-079
aggregate regional part of brain3.69e-079
collection of basal ganglia3.69e-079
cerebral subcortex3.69e-079
developing anatomical structure4.23e-07581
somite4.98e-0771
presomitic mesoderm4.98e-0771
presumptive segmental plate4.98e-0771
dermomyotome4.98e-0771
trunk paraxial mesoderm4.98e-0771
segmental subdivision of nervous system6.88e-0713


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
BHLHE40#8553217.9487254187910.004747812859838950.022317797608638
HNF4G#3174211.50136901057870.01127438304921050.0413718875400194
NANOG#79923211.69791139240510.01091164951956080.0402146151518601



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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