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Coexpression cluster:C3468: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.027892685061692!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662952214895741
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.027892685061692!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662952214895741
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}}
}}

Revision as of 16:09, 26 November 2012


Full id: C3468_non_iPS_pons_H9_teratocarcinoma_caudate_brain



Phase1 CAGE Peaks

Hg19::chr14:96342981..96343004,+p2@LOC100507043
Hg19::chr14:96343050..96343059,+p4@LOC100507043
Hg19::chr14:96343100..96343115,+p1@LOC100507043


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
embryonic stem cell4.37e-225
neuron4.68e-076
neuroblast4.68e-076
electrically signaling cell4.68e-076
Uber Anatomy
Ontology termp-valuen
neural tube2.85e-4856
neural rod2.85e-4856
future spinal cord2.85e-4856
neural keel2.85e-4856
central nervous system3.31e-4881
regional part of nervous system1.15e-4353
regional part of brain1.15e-4353
nervous system1.04e-4289
brain6.67e-3868
future brain6.67e-3868
regional part of forebrain1.42e-3641
forebrain1.42e-3641
anterior neural tube1.42e-3641
future forebrain1.42e-3641
telencephalon3.05e-3634
neural plate3.87e-3682
presumptive neural plate3.87e-3682
cerebral hemisphere1.18e-3432
neurectoderm3.81e-3486
brain grey matter2.09e-3234
gray matter2.09e-3234
regional part of telencephalon1.12e-3032
pre-chordal neural plate3.38e-2861
ecto-epithelium4.65e-27104
cerebral cortex2.04e-2625
pallium2.04e-2625
regional part of cerebral cortex6.12e-2622
neocortex2.09e-2420
structure with developmental contribution from neural crest1.79e-21132
ectoderm-derived structure3.26e-20171
ectoderm3.26e-20171
presumptive ectoderm3.26e-20171
adult organism4.62e-17114
organ system subdivision8.41e-15223
parietal lobe4.07e-135
posterior neural tube1.72e-1215
chordal neural plate1.72e-1215
tube1.35e-10192
gyrus1.79e-106
segmental subdivision of hindbrain2.44e-0812
hindbrain2.44e-0812
presumptive hindbrain2.44e-0812
limbic system9.56e-085
segmental subdivision of nervous system1.13e-0713
regional part of metencephalon1.34e-079
metencephalon1.34e-079
future metencephalon1.34e-079
neural nucleus1.53e-079
nucleus of brain1.53e-079
basal ganglion1.82e-079
nuclear complex of neuraxis1.82e-079
aggregate regional part of brain1.82e-079
collection of basal ganglia1.82e-079
cerebral subcortex1.82e-079
anatomical conduit3.28e-07240
organ part6.09e-07218


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#1066435.360256373075030.0064925092527670.027892685061692
RAD21#5885310.35503389545630.0009004912073565420.00662952214895741



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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