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Coexpression cluster:C2309: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!5.56e-19!79;UBERON:0007798!5.56e-19!79;UBERON:0003914!6.33e-19!118;UBERON:0005256!8.04e-18!143;UBERON:0004535!2.15e-16!110;UBERON:0001009!9.49e-16!113;UBERON:0001981!1.95e-15!60;UBERON:0007500!1.95e-15!60;UBERON:0004537!1.95e-15!60;UBERON:0006965!1.95e-15!60;UBERON:0000055!2.19e-15!69;UBERON:0000468!2.76e-14!659;UBERON:0004872!2.90e-14!84;UBERON:0000467!1.87e-13!625;UBERON:0002100!3.59e-13!216;UBERON:0000480!4.19e-13!626;UBERON:0001637!1.85e-12!42;UBERON:0003509!1.85e-12!42;UBERON:0004572!1.85e-12!42;UBERON:0000490!4.92e-12!138;UBERON:0000914!1.48e-11!83;UBERON:0002329!1.48e-11!83;UBERON:0003077!1.48e-11!83;UBERON:0003059!1.48e-11!83;UBERON:0007282!1.48e-11!83;UBERON:0009618!1.48e-11!83;UBERON:0007285!1.48e-11!83;UBERON:0000486!2.78e-11!82;UBERON:0000926!7.55e-11!448;UBERON:0004120!7.55e-11!448;UBERON:0006603!7.55e-11!448;UBERON:0000119!1.94e-10!312;UBERON:0004290!1.94e-10!70;UBERON:0000483!4.29e-10!309;UBERON:0000475!6.12e-10!365;UBERON:0002385!8.22e-10!63;UBERON:0001015!8.22e-10!63;UBERON:0000383!8.22e-10!63;UBERON:0001134!9.75e-10!61;UBERON:0002036!9.75e-10!61;UBERON:0003082!9.75e-10!61;UBERON:0004573!1.55e-09!33;UBERON:0004571!1.55e-09!33;UBERON:0002050!3.90e-09!605;UBERON:0005423!3.90e-09!605;UBERON:0003104!3.94e-09!238;UBERON:0009142!3.94e-09!238;UBERON:0000923!5.16e-09!604;UBERON:0005291!5.16e-09!604;UBERON:0006598!5.16e-09!604;UBERON:0002532!5.16e-09!604;UBERON:0003102!7.40e-09!95;UBERON:0000922!1.09e-08!612;UBERON:0003081!1.47e-08!216;UBERON:0000481!8.14e-08!347;UBERON:0003064!1.08e-07!37;UBERON:0004876!1.25e-07!20;UBERON:0004211!2.00e-07!16;UBERON:0001285!2.00e-07!16;UBERON:0007684!2.00e-07!16;UBERON:0003220!2.00e-07!16;UBERON:0004208!2.00e-07!16;UBERON:0000353!2.15e-07!17;UBERON:0000080!3.58e-07!18;UBERON:0002120!3.58e-07!18;UBERON:0004875!3.58e-07!18;UBERON:0005721!3.58e-07!18;UBERON:0005754!3.58e-07!18;UBERON:0007297!3.58e-07!18;UBERON:0006555!4.15e-07!17;UBERON:0005103!4.15e-07!17;UBERON:0000083!4.15e-07!17;UBERON:0009201!4.15e-07!17;UBERON:0004819!4.15e-07!17;UBERON:0006553!4.15e-07!17;UBERON:0003074!4.15e-07!17;UBERON:0003060!4.15e-07!17;UBERON:0004111!5.31e-07!241;UBERON:0005085!7.07e-07!29
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}}
}}

Revision as of 18:11, 8 August 2012


Full id: C2309_hepatic_Fibroblast_Hepatic_Smooth_Urothelial_aorta_Olfactory



Phase1 CAGE Peaks

Hg19::chr14:69445930..69445948,-p3@ACTN1
Hg19::chr14:69445968..69445984,-p2@ACTN1
Hg19::chr14:69445991..69446029,-p1@ACTN1
Hg19::chr14:69446034..69446048,-p4@ACTN1


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
vasculature5.56e-1979
vascular system5.56e-1979
epithelial tube6.33e-19118
trunk mesenchyme8.04e-18143
cardiovascular system2.15e-16110
circulatory system9.49e-16113
blood vessel1.95e-1560
epithelial tube open at both ends1.95e-1560
blood vasculature1.95e-1560
vascular cord1.95e-1560
vessel2.19e-1569
multi-cellular organism2.76e-14659
splanchnic layer of lateral plate mesoderm2.90e-1484
anatomical system1.87e-13625
trunk3.59e-13216
anatomical group4.19e-13626
artery1.85e-1242
arterial blood vessel1.85e-1242
arterial system1.85e-1242
unilaminar epithelium4.92e-12138
somite1.48e-1183
paraxial mesoderm1.48e-1183
presomitic mesoderm1.48e-1183
presumptive segmental plate1.48e-1183
trunk paraxial mesoderm1.48e-1183
presumptive paraxial mesoderm1.48e-1183
multilaminar epithelium2.78e-1182
mesoderm7.55e-11448
mesoderm-derived structure7.55e-11448
presumptive mesoderm7.55e-11448
cell layer1.94e-10312
dermomyotome1.94e-1070
epithelium4.29e-10309
organism subdivision6.12e-10365
muscle tissue8.22e-1063
musculature8.22e-1063
musculature of body8.22e-1063
skeletal muscle tissue9.75e-1061
striated muscle tissue9.75e-1061
myotome9.75e-1061
systemic artery1.55e-0933
systemic arterial system1.55e-0933
embryonic structure3.90e-09605
developing anatomical structure3.90e-09605
mesenchyme3.94e-09238
entire embryonic mesenchyme3.94e-09238
germ layer5.16e-09604
embryonic tissue5.16e-09604
presumptive structure5.16e-09604
epiblast (generic)5.16e-09604
surface structure7.40e-0995
embryo1.09e-08612
lateral plate mesoderm1.47e-08216
multi-tissue structure8.14e-08347
intermediate mesoderm1.08e-0737
urogenital ridge1.25e-0720
nephron epithelium2.00e-0716
nephron2.00e-0716
uriniferous tubule2.00e-0716
metanephric mesenchyme2.00e-0716
nephrogenic mesenchyme2.00e-0716
parenchyma2.15e-0717
mesonephros3.58e-0718
pronephros3.58e-0718
nephrogenic cord3.58e-0718
pronephric mesoderm3.58e-0718
rostral part of nephrogenic cord3.58e-0718
presumptive pronephric mesoderm3.58e-0718
excretory tube4.15e-0717
mesonephric epithelium4.15e-0717
mesonephric tubule4.15e-0717
nephric duct4.15e-0717
kidney epithelium4.15e-0717
renal duct4.15e-0717
mesonephric duct4.15e-0717
pronephric duct4.15e-0717
anatomical conduit5.31e-07241


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.

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