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Coexpression cluster:C2788: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!2.20e-07!14
|ontology_enrichment_disease=DOID:2394!2.20e-07!14
|ontology_enrichment_uberon=UBERON:0000914!3.94e-22!83;UBERON:0002329!3.94e-22!83;UBERON:0003077!3.94e-22!83;UBERON:0003059!3.94e-22!83;UBERON:0007282!3.94e-22!83;UBERON:0009618!3.94e-22!83;UBERON:0007285!3.94e-22!83;UBERON:0000486!1.03e-21!82;UBERON:0000475!1.50e-21!365;UBERON:0002100!1.77e-19!216;UBERON:0005256!4.06e-19!143;UBERON:0004290!4.77e-18!70;UBERON:0003102!2.65e-16!95;UBERON:0001134!3.91e-15!61;UBERON:0002036!3.91e-15!61;UBERON:0003082!3.91e-15!61;UBERON:0002385!9.15e-15!63;UBERON:0001015!9.15e-15!63;UBERON:0000383!9.15e-15!63;UBERON:0001637!8.63e-14!42;UBERON:0003509!8.63e-14!42;UBERON:0004572!8.63e-14!42;UBERON:0004872!1.73e-13!84;UBERON:0001981!4.05e-13!60;UBERON:0007500!4.05e-13!60;UBERON:0004537!4.05e-13!60;UBERON:0006965!4.05e-13!60;UBERON:0000483!5.11e-13!309;UBERON:0000481!5.58e-13!347;UBERON:0000119!6.04e-13!312;UBERON:0000055!6.23e-13!69;UBERON:0000468!6.60e-13!659;UBERON:0003104!1.79e-12!238;UBERON:0009142!1.79e-12!238;UBERON:0002049!4.88e-12!79;UBERON:0007798!4.88e-12!79;UBERON:0000490!5.66e-12!138;UBERON:0003914!2.40e-11!118;UBERON:0004573!2.66e-11!33;UBERON:0004571!2.66e-11!33;UBERON:0000467!3.38e-11!625;UBERON:0000480!5.77e-11!626;UBERON:0002199!5.41e-10!45;UBERON:0002416!5.41e-10!45;UBERON:0000477!1.25e-09!286;UBERON:0002097!3.52e-09!40;UBERON:0004111!6.54e-09!241;UBERON:0001009!1.50e-07!113;UBERON:0004535!1.60e-07!110
|ontology_enrichment_uberon=UBERON:0000914!3.94e-22!83;UBERON:0002329!3.94e-22!83;UBERON:0003077!3.94e-22!83;UBERON:0003059!3.94e-22!83;UBERON:0007282!3.94e-22!83;UBERON:0009618!3.94e-22!83;UBERON:0007285!3.94e-22!83;UBERON:0000486!1.03e-21!82;UBERON:0000475!1.50e-21!365;UBERON:0002100!1.77e-19!216;UBERON:0005256!4.06e-19!143;UBERON:0004290!4.77e-18!70;UBERON:0003102!2.65e-16!95;UBERON:0001134!3.91e-15!61;UBERON:0002036!3.91e-15!61;UBERON:0003082!3.91e-15!61;UBERON:0002385!9.15e-15!63;UBERON:0001015!9.15e-15!63;UBERON:0000383!9.15e-15!63;UBERON:0001637!8.63e-14!42;UBERON:0003509!8.63e-14!42;UBERON:0004572!8.63e-14!42;UBERON:0004872!1.73e-13!84;UBERON:0001981!4.05e-13!60;UBERON:0007500!4.05e-13!60;UBERON:0004537!4.05e-13!60;UBERON:0006965!4.05e-13!60;UBERON:0000483!5.11e-13!309;UBERON:0000481!5.58e-13!347;UBERON:0000119!6.04e-13!312;UBERON:0000055!6.23e-13!69;UBERON:0000468!6.60e-13!659;UBERON:0003104!1.79e-12!238;UBERON:0009142!1.79e-12!238;UBERON:0002049!4.88e-12!79;UBERON:0007798!4.88e-12!79;UBERON:0000490!5.66e-12!138;UBERON:0003914!2.40e-11!118;UBERON:0004573!2.66e-11!33;UBERON:0004571!2.66e-11!33;UBERON:0000467!3.38e-11!625;UBERON:0000480!5.77e-11!626;UBERON:0002199!5.41e-10!45;UBERON:0002416!5.41e-10!45;UBERON:0000477!1.25e-09!286;UBERON:0002097!3.52e-09!40;UBERON:0004111!6.54e-09!241;UBERON:0001009!1.50e-07!113;UBERON:0004535!1.60e-07!110
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819187957473469!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106724658277819!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323031965520033
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}}
}}

Revision as of 14:18, 5 September 2012


Full id: C2788_Urothelial_Fibroblast_Small_Smooth_Mallassezderived_Myoblast_Gingival



Phase1 CAGE Peaks

Hg19::chr4:177713756..177713777,-p4@VEGFC
Hg19::chr4:177713788..177713805,-p6@VEGFC
Hg19::chr4:177714068..177714085,-p1@VEGFC
Hg19::chr4:177714098..177714111,-p3@VEGFC


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
somite3.94e-2283
paraxial mesoderm3.94e-2283
presomitic mesoderm3.94e-2283
presumptive segmental plate3.94e-2283
trunk paraxial mesoderm3.94e-2283
presumptive paraxial mesoderm3.94e-2283
multilaminar epithelium1.03e-2182
organism subdivision1.50e-21365
trunk1.77e-19216
trunk mesenchyme4.06e-19143
dermomyotome4.77e-1870
surface structure2.65e-1695
skeletal muscle tissue3.91e-1561
striated muscle tissue3.91e-1561
myotome3.91e-1561
muscle tissue9.15e-1563
musculature9.15e-1563
musculature of body9.15e-1563
artery8.63e-1442
arterial blood vessel8.63e-1442
arterial system8.63e-1442
splanchnic layer of lateral plate mesoderm1.73e-1384
blood vessel4.05e-1360
epithelial tube open at both ends4.05e-1360
blood vasculature4.05e-1360
vascular cord4.05e-1360
epithelium5.11e-13309
multi-tissue structure5.58e-13347
cell layer6.04e-13312
vessel6.23e-1369
multi-cellular organism6.60e-13659
mesenchyme1.79e-12238
entire embryonic mesenchyme1.79e-12238
vasculature4.88e-1279
vascular system4.88e-1279
unilaminar epithelium5.66e-12138
epithelial tube2.40e-11118
systemic artery2.66e-1133
systemic arterial system2.66e-1133
anatomical system3.38e-11625
anatomical group5.77e-11626
integument5.41e-1045
integumental system5.41e-1045
anatomical cluster1.25e-09286
skin of body3.52e-0940
anatomical conduit6.54e-09241
circulatory system1.50e-07113
cardiovascular system1.60e-07110
Disease
Ontology termp-valuen
ovarian cancer2.20e-0714


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#1066445.360256373075030.001211145381643620.00819187957473469
E2F1#186944.907389214879320.001724022357361790.0106724658277819
TAF1#687243.343046285745290.008005664898701650.0323031965520033



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.