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Coexpression cluster:C1664: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249531267308724!CTCFL#140690;5:19.7464743589744:3.32745051287657e-07:1.65641374697005e-05!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130584396433924!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256710089492077!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00238818628588154!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00116942925910808!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.000229340599759633!SMC3#9126;5:15.0449328449328:1.29633924985553e-06:5.15568830600387e-05!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000574107310107559!ZNF143#7702;5:13.5008765522279:2.22790360787208e-06:7.97395561694831e-05!ZNF263#10127;5:8.22184163701068:2.6606316672286e-05:0.000570699754967525
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249531267308724!CTCFL#140690;5:19.7464743589744:3.32745051287657e-07:1.65641374697005e-05!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130584396433924!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256710089492077!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00238818628588154!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00116942925910808!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.000229340599759633!SMC3#9126;5:15.0449328449328:1.29633924985553e-06:5.15568830600387e-05!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000574107310107559!ZNF143#7702;5:13.5008765522279:2.22790360787208e-06:7.97395561694831e-05!ZNF263#10127;5:8.22184163701068:2.6606316672286e-05:0.000570699754967525
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}}
}}

Revision as of 15:01, 26 November 2012


Full id: C1664_uterus_epididymis_aorta_cervix_caudate_Adipocyte_ductus



Phase1 CAGE Peaks

Hg19::chr12:15374234..15374247,-p3@RERG
Hg19::chr12:15374258..15374265,-p5@RERG
Hg19::chr12:15374283..15374294,-p4@RERG
Hg19::chr12:15374328..15374342,-p2@RERG
Hg19::chr12:15374343..15374416,-p1@RERG


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 organism1.58e-66114
neural tube8.89e-3056
neural rod8.89e-3056
future spinal cord8.89e-3056
neural keel8.89e-3056
regional part of nervous system8.28e-2853
regional part of brain8.28e-2853
brain6.33e-2568
future brain6.33e-2568
central nervous system1.71e-2481
regional part of forebrain2.68e-2441
forebrain2.68e-2441
anterior neural tube2.68e-2441
future forebrain2.68e-2441
organ system subdivision1.15e-22223
nervous system4.42e-2289
cerebral hemisphere1.08e-2132
telencephalon3.12e-2134
brain grey matter3.89e-2134
gray matter3.89e-2134
neural plate4.56e-2182
presumptive neural plate4.56e-2182
neurectoderm3.76e-2086
regional part of telencephalon6.28e-2032
regional part of cerebral cortex6.13e-1922
neocortex1.79e-1720
ecto-epithelium2.94e-16104
structure with developmental contribution from neural crest4.60e-16132
cerebral cortex7.75e-1625
pallium7.75e-1625
multi-tissue structure1.61e-15342
pre-chordal neural plate1.49e-1461
anatomical cluster2.53e-14373
organ part4.40e-13218
ectoderm-derived structure1.63e-11171
ectoderm1.63e-11171
presumptive ectoderm1.63e-11171
organ4.47e-11503
multi-cellular organism1.16e-09656
embryo1.23e-08592
tube1.42e-08192
developing anatomical structure5.36e-08581
anatomical conduit1.35e-07240
gyrus4.24e-076
embryonic structure6.16e-07564
basal ganglion7.76e-079
nuclear complex of neuraxis7.76e-079
aggregate regional part of brain7.76e-079
collection of basal ganglia7.76e-079
cerebral subcortex7.76e-079
posterior neural tube8.00e-0715
chordal neural plate8.00e-0715
germ layer8.22e-07560
germ layer / neural crest8.22e-07560
embryonic tissue8.22e-07560
presumptive structure8.22e-07560
germ layer / neural crest derived structure8.22e-07560
epiblast (generic)8.22e-07560
neural nucleus9.31e-079
nucleus of brain9.31e-079


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#1066455.360256373075030.0002259278299937090.00249531267308724
CTCFL#140690519.74647435897443.32745051287657e-071.65641374697005e-05
MAX#414956.452555509007128.93743970843928e-050.00130584396433924
MYC#460944.177825497287520.005691969036823440.0256710089492077
NFKB1#479055.488063424193840.0002008162847462320.00238818628588154
PAX5#507956.669565531177837.57493746384605e-050.00116942925910808
RAD21#5885510.35503389545638.39503550283973e-060.000229340599759633
SMC3#9126515.04493284493281.29633924985553e-065.15568830600387e-05
SPI1#668858.204323508522732.68916109982495e-050.000574107310107559
ZNF143#7702513.50087655222792.22790360787208e-067.97395561694831e-05
ZNF263#1012758.221841637010682.6606316672286e-050.000570699754967525



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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