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Coexpression cluster:C776: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!2.33e-08!14
|ontology_enrichment_disease=DOID:2394!2.33e-08!14
|ontology_enrichment_uberon=UBERON:0001134!2.95e-20!61;UBERON:0002036!2.95e-20!61;UBERON:0003082!2.95e-20!61;UBERON:0000914!2.30e-19!83;UBERON:0002329!2.30e-19!83;UBERON:0003077!2.30e-19!83;UBERON:0003059!2.30e-19!83;UBERON:0007282!2.30e-19!83;UBERON:0009618!2.30e-19!83;UBERON:0007285!2.30e-19!83;UBERON:0004290!2.79e-19!70;UBERON:0002385!7.77e-19!63;UBERON:0001015!7.77e-19!63;UBERON:0000383!7.77e-19!63;UBERON:0000486!4.25e-16!82;UBERON:0004872!7.66e-14!84;UBERON:0001637!3.35e-13!42;UBERON:0003509!3.35e-13!42;UBERON:0004572!3.35e-13!42;UBERON:0005256!1.95e-12!143;UBERON:0004573!2.91e-12!33;UBERON:0004571!2.91e-12!33;UBERON:0002049!1.34e-10!79;UBERON:0007798!1.34e-10!79;UBERON:0002100!4.11e-10!216;UBERON:0001009!6.69e-10!113;UBERON:0001981!8.59e-10!60;UBERON:0007500!8.59e-10!60;UBERON:0004537!8.59e-10!60;UBERON:0006965!8.59e-10!60;UBERON:0004535!1.02e-09!110;UBERON:0000948!1.88e-09!24;UBERON:0005498!1.88e-09!24;UBERON:0004140!1.88e-09!24;UBERON:0009881!1.88e-09!24;UBERON:0004141!1.88e-09!24;UBERON:0003084!1.88e-09!24;UBERON:0007005!1.88e-09!24;UBERON:0004139!1.88e-09!24;UBERON:0004291!1.88e-09!24;UBERON:0007100!2.73e-09!27;UBERON:0000490!1.51e-08!138;UBERON:0003914!2.24e-08!118;UBERON:0000481!2.47e-08!347;UBERON:0003104!3.80e-08!238;UBERON:0009142!3.80e-08!238;UBERON:0004237!4.41e-08!10;UBERON:0004695!4.41e-08!10;UBERON:0002111!4.41e-08!10;UBERON:0004178!4.41e-08!10;UBERON:0000475!7.50e-08!365;UBERON:0000055!1.05e-07!69;UBERON:0001135!1.35e-07!15
|ontology_enrichment_uberon=UBERON:0001134!2.95e-20!61;UBERON:0002036!2.95e-20!61;UBERON:0003082!2.95e-20!61;UBERON:0000914!2.30e-19!83;UBERON:0002329!2.30e-19!83;UBERON:0003077!2.30e-19!83;UBERON:0003059!2.30e-19!83;UBERON:0007282!2.30e-19!83;UBERON:0009618!2.30e-19!83;UBERON:0007285!2.30e-19!83;UBERON:0004290!2.79e-19!70;UBERON:0002385!7.77e-19!63;UBERON:0001015!7.77e-19!63;UBERON:0000383!7.77e-19!63;UBERON:0000486!4.25e-16!82;UBERON:0004872!7.66e-14!84;UBERON:0001637!3.35e-13!42;UBERON:0003509!3.35e-13!42;UBERON:0004572!3.35e-13!42;UBERON:0005256!1.95e-12!143;UBERON:0004573!2.91e-12!33;UBERON:0004571!2.91e-12!33;UBERON:0002049!1.34e-10!79;UBERON:0007798!1.34e-10!79;UBERON:0002100!4.11e-10!216;UBERON:0001009!6.69e-10!113;UBERON:0001981!8.59e-10!60;UBERON:0007500!8.59e-10!60;UBERON:0004537!8.59e-10!60;UBERON:0006965!8.59e-10!60;UBERON:0004535!1.02e-09!110;UBERON:0000948!1.88e-09!24;UBERON:0005498!1.88e-09!24;UBERON:0004140!1.88e-09!24;UBERON:0009881!1.88e-09!24;UBERON:0004141!1.88e-09!24;UBERON:0003084!1.88e-09!24;UBERON:0007005!1.88e-09!24;UBERON:0004139!1.88e-09!24;UBERON:0004291!1.88e-09!24;UBERON:0007100!2.73e-09!27;UBERON:0000490!1.51e-08!138;UBERON:0003914!2.24e-08!118;UBERON:0000481!2.47e-08!347;UBERON:0003104!3.80e-08!238;UBERON:0009142!3.80e-08!238;UBERON:0004237!4.41e-08!10;UBERON:0004695!4.41e-08!10;UBERON:0002111!4.41e-08!10;UBERON:0004178!4.41e-08!10;UBERON:0000475!7.50e-08!365;UBERON:0000055!1.05e-07!69;UBERON:0001135!1.35e-07!15
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}}
}}

Revision as of 20:48, 8 August 2012


Full id: C776_chorionic_placenta_Smooth_Aortic_Fibroblast_leiomyoma_mesothelioma



Phase1 CAGE Peaks

Hg19::chr9:118916228..118916241,+p18@PAPPA
Hg19::chr9:118916249..118916260,+p11@PAPPA
Hg19::chr9:118950325..118950341,+p22@PAPPA
Hg19::chr9:118973954..118973965,+p@chr9:118973954..118973965
+
Hg19::chr9:119094607..119094618,+p50@PAPPA
Hg19::chr9:119160527..119160548,+p@chr9:119160527..119160548
+
Hg19::chr9:119160571..119160596,+p@chr9:119160571..119160596
+
Hg19::chr9:119160673..119160717,+p@chr9:119160673..119160717
+
Hg19::chr9:119161224..119161240,+p17@PAPPA
Hg19::chr9:119162143..119162169,+p14@PAPPA
Hg19::chr9:119163686..119163705,+p10@PAPPA


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 tissue2.95e-2061
striated muscle tissue2.95e-2061
myotome2.95e-2061
somite2.30e-1983
paraxial mesoderm2.30e-1983
presomitic mesoderm2.30e-1983
presumptive segmental plate2.30e-1983
trunk paraxial mesoderm2.30e-1983
presumptive paraxial mesoderm2.30e-1983
dermomyotome2.79e-1970
muscle tissue7.77e-1963
musculature7.77e-1963
musculature of body7.77e-1963
multilaminar epithelium4.25e-1682
splanchnic layer of lateral plate mesoderm7.66e-1484
artery3.35e-1342
arterial blood vessel3.35e-1342
arterial system3.35e-1342
trunk mesenchyme1.95e-12143
systemic artery2.91e-1233
systemic arterial system2.91e-1233
vasculature1.34e-1079
vascular system1.34e-1079
trunk4.11e-10216
circulatory system6.69e-10113
blood vessel8.59e-1060
epithelial tube open at both ends8.59e-1060
blood vasculature8.59e-1060
vascular cord8.59e-1060
cardiovascular system1.02e-09110
heart1.88e-0924
primitive heart tube1.88e-0924
primary heart field1.88e-0924
anterior lateral plate mesoderm1.88e-0924
heart tube1.88e-0924
heart primordium1.88e-0924
cardiac mesoderm1.88e-0924
cardiogenic plate1.88e-0924
heart rudiment1.88e-0924
primary circulatory organ2.73e-0927
unilaminar epithelium1.51e-08138
epithelial tube2.24e-08118
multi-tissue structure2.47e-08347
mesenchyme3.80e-08238
entire embryonic mesenchyme3.80e-08238
blood vessel smooth muscle4.41e-0810
arterial system smooth muscle4.41e-0810
artery smooth muscle tissue4.41e-0810
aorta smooth muscle tissue4.41e-0810
organism subdivision7.50e-08365
vessel1.05e-0769
smooth muscle tissue1.35e-0715
Disease
Ontology termp-valuen
ovarian cancer2.33e-0814


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)

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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


No analysis results for this cluster

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.