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Coexpression cluster:C1948: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002385!6.82e-18!63;UBERON:0001015!6.82e-18!63;UBERON:0000383!6.82e-18!63;UBERON:0001134!2.15e-17!61;UBERON:0002036!2.15e-17!61;UBERON:0003082!2.15e-17!61;UBERON:0004290!7.38e-16!70;UBERON:0000914!9.69e-16!83;UBERON:0002329!9.69e-16!83;UBERON:0003077!9.69e-16!83;UBERON:0003059!9.69e-16!83;UBERON:0007282!9.69e-16!83;UBERON:0009618!9.69e-16!83;UBERON:0007285!9.69e-16!83;UBERON:0000486!8.21e-14!82;UBERON:0000481!3.05e-11!347;UBERON:0001637!1.51e-10!42;UBERON:0003509!1.51e-10!42;UBERON:0004572!1.51e-10!42;UBERON:0000922!4.43e-10!612;UBERON:0002050!7.39e-10!605;UBERON:0005423!7.39e-10!605;UBERON:0000923!9.80e-10!604;UBERON:0005291!9.80e-10!604;UBERON:0006598!9.80e-10!604;UBERON:0002532!9.80e-10!604;UBERON:0000468!1.48e-09!659;UBERON:0005256!6.43e-09!143;UBERON:0000480!7.66e-09!626;UBERON:0004573!8.58e-09!33;UBERON:0004571!8.58e-09!33;UBERON:0000467!9.95e-09!625;UBERON:0007100!1.70e-08!27;UBERON:0004872!2.11e-08!84;UBERON:0000475!4.05e-08!365;UBERON:0003104!6.39e-08!238;UBERON:0009142!6.39e-08!238;UBERON:0000490!6.71e-08!138;UBERON:0000948!7.46e-08!24;UBERON:0005498!7.46e-08!24;UBERON:0004140!7.46e-08!24;UBERON:0009881!7.46e-08!24;UBERON:0004141!7.46e-08!24;UBERON:0003084!7.46e-08!24;UBERON:0007005!7.46e-08!24;UBERON:0004139!7.46e-08!24;UBERON:0004291!7.46e-08!24;UBERON:0002049!1.35e-07!79;UBERON:0007798!1.35e-07!79;UBERON:0002100!1.78e-07!216;UBERON:0001009!3.13e-07!113;UBERON:0000483!4.80e-07!309;UBERON:0001981!5.09e-07!60;UBERON:0007500!5.09e-07!60;UBERON:0004537!5.09e-07!60;UBERON:0006965!5.09e-07!60
|ontology_enrichment_uberon=UBERON:0002385!6.82e-18!63;UBERON:0001015!6.82e-18!63;UBERON:0000383!6.82e-18!63;UBERON:0001134!2.15e-17!61;UBERON:0002036!2.15e-17!61;UBERON:0003082!2.15e-17!61;UBERON:0004290!7.38e-16!70;UBERON:0000914!9.69e-16!83;UBERON:0002329!9.69e-16!83;UBERON:0003077!9.69e-16!83;UBERON:0003059!9.69e-16!83;UBERON:0007282!9.69e-16!83;UBERON:0009618!9.69e-16!83;UBERON:0007285!9.69e-16!83;UBERON:0000486!8.21e-14!82;UBERON:0000481!3.05e-11!347;UBERON:0001637!1.51e-10!42;UBERON:0003509!1.51e-10!42;UBERON:0004572!1.51e-10!42;UBERON:0000922!4.43e-10!612;UBERON:0002050!7.39e-10!605;UBERON:0005423!7.39e-10!605;UBERON:0000923!9.80e-10!604;UBERON:0005291!9.80e-10!604;UBERON:0006598!9.80e-10!604;UBERON:0002532!9.80e-10!604;UBERON:0000468!1.48e-09!659;UBERON:0005256!6.43e-09!143;UBERON:0000480!7.66e-09!626;UBERON:0004573!8.58e-09!33;UBERON:0004571!8.58e-09!33;UBERON:0000467!9.95e-09!625;UBERON:0007100!1.70e-08!27;UBERON:0004872!2.11e-08!84;UBERON:0000475!4.05e-08!365;UBERON:0003104!6.39e-08!238;UBERON:0009142!6.39e-08!238;UBERON:0000490!6.71e-08!138;UBERON:0000948!7.46e-08!24;UBERON:0005498!7.46e-08!24;UBERON:0004140!7.46e-08!24;UBERON:0009881!7.46e-08!24;UBERON:0004141!7.46e-08!24;UBERON:0003084!7.46e-08!24;UBERON:0007005!7.46e-08!24;UBERON:0004139!7.46e-08!24;UBERON:0004291!7.46e-08!24;UBERON:0002049!1.35e-07!79;UBERON:0007798!1.35e-07!79;UBERON:0002100!1.78e-07!216;UBERON:0001009!3.13e-07!113;UBERON:0000483!4.80e-07!309;UBERON:0001981!5.09e-07!60;UBERON:0007500!5.09e-07!60;UBERON:0004537!5.09e-07!60;UBERON:0006965!5.09e-07!60
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}}
}}

Revision as of 12:43, 5 September 2012


Full id: C1948_mesenchymal_Smooth_Skeletal_Lens_Keratocytes_cervical_salivary



Phase1 CAGE Peaks

Hg19::chr5:110409038..110409052,+p4@TSLP
Hg19::chr5:110409053..110409100,+p1@TSLP
Hg19::chr5:110409111..110409126,+p2@TSLP
Hg19::chr5:110409130..110409145,+p5@TSLP
Hg19::chr5:110409170..110409189,+p6@TSLP


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>

Uber Anatomy
Ontology termp-valuen
muscle tissue6.82e-1863
musculature6.82e-1863
musculature of body6.82e-1863
skeletal muscle tissue2.15e-1761
striated muscle tissue2.15e-1761
myotome2.15e-1761
dermomyotome7.38e-1670
somite9.69e-1683
paraxial mesoderm9.69e-1683
presomitic mesoderm9.69e-1683
presumptive segmental plate9.69e-1683
trunk paraxial mesoderm9.69e-1683
presumptive paraxial mesoderm9.69e-1683
multilaminar epithelium8.21e-1482
multi-tissue structure3.05e-11347
artery1.51e-1042
arterial blood vessel1.51e-1042
arterial system1.51e-1042
embryo4.43e-10612
embryonic structure7.39e-10605
developing anatomical structure7.39e-10605
germ layer9.80e-10604
embryonic tissue9.80e-10604
presumptive structure9.80e-10604
epiblast (generic)9.80e-10604
multi-cellular organism1.48e-09659
trunk mesenchyme6.43e-09143
anatomical group7.66e-09626
systemic artery8.58e-0933
systemic arterial system8.58e-0933
anatomical system9.95e-09625
primary circulatory organ1.70e-0827
splanchnic layer of lateral plate mesoderm2.11e-0884
organism subdivision4.05e-08365
mesenchyme6.39e-08238
entire embryonic mesenchyme6.39e-08238
unilaminar epithelium6.71e-08138
heart7.46e-0824
primitive heart tube7.46e-0824
primary heart field7.46e-0824
anterior lateral plate mesoderm7.46e-0824
heart tube7.46e-0824
heart primordium7.46e-0824
cardiac mesoderm7.46e-0824
cardiogenic plate7.46e-0824
heart rudiment7.46e-0824
vasculature1.35e-0779
vascular system1.35e-0779
trunk1.78e-07216
circulatory system3.13e-07113
epithelium4.80e-07309
blood vessel5.09e-0760
epithelial tube open at both ends5.09e-0760
blood vasculature5.09e-0760
vascular cord5.09e-0760


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#1066455.360256373075030.0002259278299937090.00250166206920196
EGR1#195854.988179094810140.0003237398000590710.00331026639694237
HMGN3#932458.178547723350592.73180911341838e-050.00058273572711663
IRF1#365957.63716375356393.84754333311872e-050.000724938802395069
PAX5#507956.669565531177837.57493746384605e-050.00117133386702194
RAD21#5885510.35503389545638.39503550283973e-060.000229821523690977
SPI1#668858.204323508522732.68916109982495e-050.000575401139325175
ZNF263#1012758.221841637010682.6606316672286e-050.000572227575563608



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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