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Coexpression cluster:C855: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!9.38e-09!14
|ontology_enrichment_disease=DOID:2394!9.38e-09!14
|ontology_enrichment_uberon=UBERON:0001134!9.25e-20!61;UBERON:0002036!9.25e-20!61;UBERON:0003082!9.25e-20!61;UBERON:0004290!1.69e-19!70;UBERON:0002385!3.68e-19!63;UBERON:0001015!3.68e-19!63;UBERON:0000383!3.68e-19!63;UBERON:0000490!2.99e-16!138;UBERON:0000486!8.99e-16!82;UBERON:0000914!2.63e-15!83;UBERON:0002329!2.63e-15!83;UBERON:0003077!2.63e-15!83;UBERON:0003059!2.63e-15!83;UBERON:0007282!2.63e-15!83;UBERON:0009618!2.63e-15!83;UBERON:0007285!2.63e-15!83;UBERON:0004872!4.49e-15!84;UBERON:0004535!1.53e-13!110;UBERON:0001009!2.52e-13!113;UBERON:0005256!7.56e-12!143;UBERON:0001637!4.02e-10!42;UBERON:0003509!4.02e-10!42;UBERON:0004572!4.02e-10!42;UBERON:0004573!4.27e-09!33;UBERON:0004571!4.27e-09!33;UBERON:0003914!4.73e-09!118;UBERON:0002049!7.34e-09!79;UBERON:0007798!7.34e-09!79;UBERON:0001981!1.13e-08!60;UBERON:0007500!1.13e-08!60;UBERON:0004537!1.13e-08!60;UBERON:0006965!1.13e-08!60;UBERON:0000055!6.17e-08!69;UBERON:0000948!3.77e-07!24;UBERON:0005498!3.77e-07!24;UBERON:0004140!3.77e-07!24;UBERON:0009881!3.77e-07!24;UBERON:0004141!3.77e-07!24;UBERON:0003084!3.77e-07!24;UBERON:0007005!3.77e-07!24;UBERON:0004139!3.77e-07!24;UBERON:0004291!3.77e-07!24;UBERON:0002100!4.83e-07!216
|ontology_enrichment_uberon=UBERON:0001134!9.25e-20!61;UBERON:0002036!9.25e-20!61;UBERON:0003082!9.25e-20!61;UBERON:0004290!1.69e-19!70;UBERON:0002385!3.68e-19!63;UBERON:0001015!3.68e-19!63;UBERON:0000383!3.68e-19!63;UBERON:0000490!2.99e-16!138;UBERON:0000486!8.99e-16!82;UBERON:0000914!2.63e-15!83;UBERON:0002329!2.63e-15!83;UBERON:0003077!2.63e-15!83;UBERON:0003059!2.63e-15!83;UBERON:0007282!2.63e-15!83;UBERON:0009618!2.63e-15!83;UBERON:0007285!2.63e-15!83;UBERON:0004872!4.49e-15!84;UBERON:0004535!1.53e-13!110;UBERON:0001009!2.52e-13!113;UBERON:0005256!7.56e-12!143;UBERON:0001637!4.02e-10!42;UBERON:0003509!4.02e-10!42;UBERON:0004572!4.02e-10!42;UBERON:0004573!4.27e-09!33;UBERON:0004571!4.27e-09!33;UBERON:0003914!4.73e-09!118;UBERON:0002049!7.34e-09!79;UBERON:0007798!7.34e-09!79;UBERON:0001981!1.13e-08!60;UBERON:0007500!1.13e-08!60;UBERON:0004537!1.13e-08!60;UBERON:0006965!1.13e-08!60;UBERON:0000055!6.17e-08!69;UBERON:0000948!3.77e-07!24;UBERON:0005498!3.77e-07!24;UBERON:0004140!3.77e-07!24;UBERON:0009881!3.77e-07!24;UBERON:0004141!3.77e-07!24;UBERON:0003084!3.77e-07!24;UBERON:0007005!3.77e-07!24;UBERON:0004139!3.77e-07!24;UBERON:0004291!3.77e-07!24;UBERON:0002100!4.83e-07!216
|tf_chipseq_enrich=CHD2#1106;5:5.17201141705843:0.00140075061091929:0.00910971997346032!E2F1#1869;9:4.41665029339139:4.94361321523441e-06:0.000152708080622853!EBF1#1879;9:8.0158201619121:2.54528393136776e-08:1.77336163114154e-06!EP300#2033;5:3.3869708631116:0.00921626169811418:0.0348404515687315!FOXA1#3169;5:5.54070987469273:0.00102165177568981:0.00724669178221058!HDAC2#3066;5:6.70781011831313:0.000421111437944604:0.00393948920346619!IRF4#3662;9:19.7230614180697:8.19313855480698e-12:1.034683431107e-09!POLR2A#5430;9:1.93270785890226:0.00598008918360611:0.0268152734638546!SPI1#6688;9:7.38389115767045:5.27911959243962e-08:3.35981700862158e-06!TAF1#6872;9:3.00874165717076:0.000140064424388755:0.00182738143894281!USF1#7391;8:5.08919942176637:1.24116492349793e-05:0.000306516962509342!USF2#7392;9:11.6929776465626:8.80406743651317e-10:8.23913977600358e-08
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}}
}}

Revision as of 12:04, 5 September 2012


Full id: C855_Mesothelial_Fibroblast_mesenchymal_Smooth_Sertoli_Myoblast_CD4



Phase1 CAGE Peaks

Hg19::chr2:162930622..162930641,-p4@DPP4
Hg19::chr2:162930654..162930665,-p7@DPP4
Hg19::chr2:162930688..162930752,-p2@DPP4
Hg19::chr2:162930797..162930810,-p6@DPP4
Hg19::chr2:162930861..162930874,-p10@DPP4
Hg19::chr2:162931058..162931063,-p16@DPP4
Hg19::chr2:162931082..162931100,-p9@DPP4
Hg19::chr2:162931120..162931131,-p15@DPP4
Hg19::chr2:162931138..162931149,-p14@DPP4
Hg19::chr4:120060444..120060452,-p@chr4:120060444..120060452
-


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue9.25e-2061
striated muscle tissue9.25e-2061
myotome9.25e-2061
dermomyotome1.69e-1970
muscle tissue3.68e-1963
musculature3.68e-1963
musculature of body3.68e-1963
unilaminar epithelium2.99e-16138
multilaminar epithelium8.99e-1682
somite2.63e-1583
paraxial mesoderm2.63e-1583
presomitic mesoderm2.63e-1583
presumptive segmental plate2.63e-1583
trunk paraxial mesoderm2.63e-1583
presumptive paraxial mesoderm2.63e-1583
splanchnic layer of lateral plate mesoderm4.49e-1584
cardiovascular system1.53e-13110
circulatory system2.52e-13113
trunk mesenchyme7.56e-12143
artery4.02e-1042
arterial blood vessel4.02e-1042
arterial system4.02e-1042
systemic artery4.27e-0933
systemic arterial system4.27e-0933
epithelial tube4.73e-09118
vasculature7.34e-0979
vascular system7.34e-0979
blood vessel1.13e-0860
epithelial tube open at both ends1.13e-0860
blood vasculature1.13e-0860
vascular cord1.13e-0860
vessel6.17e-0869
heart3.77e-0724
primitive heart tube3.77e-0724
primary heart field3.77e-0724
anterior lateral plate mesoderm3.77e-0724
heart tube3.77e-0724
heart primordium3.77e-0724
cardiac mesoderm3.77e-0724
cardiogenic plate3.77e-0724
heart rudiment3.77e-0724
trunk4.83e-07216
Disease
Ontology termp-valuen
ovarian cancer9.38e-0914


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
CHD2#110655.172011417058430.001400750610919290.00910971997346032
E2F1#186994.416650293391394.94361321523441e-060.000152708080622853
EBF1#187998.01582016191212.54528393136776e-081.77336163114154e-06
EP300#203353.38697086311160.009216261698114180.0348404515687315
FOXA1#316955.540709874692730.001021651775689810.00724669178221058
HDAC2#306656.707810118313130.0004211114379446040.00393948920346619
IRF4#3662919.72306141806978.19313855480698e-121.034683431107e-09
POLR2A#543091.932707858902260.005980089183606110.0268152734638546
SPI1#668897.383891157670455.27911959243962e-083.35981700862158e-06
TAF1#687293.008741657170760.0001400644243887550.00182738143894281
USF1#739185.089199421766371.24116492349793e-050.000306516962509342
USF2#7392911.69297764656268.80406743651317e-108.23913977600358e-08



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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