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Coexpression cluster:C2779: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!5.78e-19!84;UBERON:0000477!8.19e-19!286;UBERON:0000475!1.63e-18!365;UBERON:0004111!1.85e-18!241;UBERON:0000119!3.27e-18!312;UBERON:0002049!6.46e-18!79;UBERON:0007798!6.46e-18!79;UBERON:0000483!7.55e-18!309;UBERON:0000468!8.47e-17!659;UBERON:0000055!1.28e-16!69;UBERON:0000914!1.81e-16!83;UBERON:0002329!1.81e-16!83;UBERON:0003077!1.81e-16!83;UBERON:0003059!1.81e-16!83;UBERON:0007282!1.81e-16!83;UBERON:0009618!1.81e-16!83;UBERON:0007285!1.81e-16!83;UBERON:0001009!4.70e-15!113;UBERON:0001981!7.74e-15!60;UBERON:0007500!7.74e-15!60;UBERON:0004537!7.74e-15!60;UBERON:0006965!7.74e-15!60;UBERON:0004535!1.16e-14!110;UBERON:0000486!1.19e-14!82;UBERON:0000467!5.43e-14!625;UBERON:0000480!9.41e-14!626;UBERON:0004290!2.21e-13!70;UBERON:0007023!3.01e-13!115;UBERON:0000025!4.81e-13!194;UBERON:0002385!1.32e-12!63;UBERON:0001015!1.32e-12!63;UBERON:0000383!1.32e-12!63;UBERON:0001134!4.10e-12!61;UBERON:0002036!4.10e-12!61;UBERON:0003082!4.10e-12!61;UBERON:0000481!4.85e-12!347;UBERON:0003914!2.87e-11!118;UBERON:0000490!7.60e-11!138;UBERON:0005256!9.85e-11!143;UBERON:0002100!3.41e-10!216;UBERON:0001637!9.78e-10!42;UBERON:0003509!9.78e-10!42;UBERON:0004572!9.78e-10!42;UBERON:0004573!2.24e-09!33;UBERON:0004571!2.24e-09!33;UBERON:0002050!3.16e-09!605;UBERON:0005423!3.16e-09!605;UBERON:0000923!3.34e-09!604;UBERON:0005291!3.34e-09!604;UBERON:0006598!3.34e-09!604;UBERON:0002532!3.34e-09!604;UBERON:0000922!6.70e-09!612;UBERON:0001986!1.30e-08!18;UBERON:0004638!1.30e-08!18;UBERON:0004852!1.30e-08!18;UBERON:0000479!1.24e-07!787;UBERON:0000947!1.68e-07!21;UBERON:0010191!1.68e-07!21;UBERON:0006914!1.89e-07!25;UBERON:0001013!2.22e-07!14;UBERON:0000033!3.17e-07!123;UBERON:0003102!3.46e-07!95;UBERON:0000153!4.85e-07!129;UBERON:0007811!4.85e-07!129;UBERON:0007100!7.06e-07!27;UBERON:0000487!9.07e-07!22
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}}
}}

Revision as of 18:35, 8 August 2012


Full id: C2779_Adipocyte_mature_adipose_Preadipocyte_Fibroblast_Mesenchymal_Hair



Phase1 CAGE Peaks

Hg19::chr4:152148941..152148953,-p3@SH3D19
Hg19::chr4:152148984..152149004,-p4@SH3D19
Hg19::chr4:152149009..152149020,-p7@SH3D19
Hg19::chr4:152149033..152149117,-p1@SH3D19


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
splanchnic layer of lateral plate mesoderm5.78e-1984
anatomical cluster8.19e-19286
organism subdivision1.63e-18365
anatomical conduit1.85e-18241
cell layer3.27e-18312
vasculature6.46e-1879
vascular system6.46e-1879
epithelium7.55e-18309
multi-cellular organism8.47e-17659
vessel1.28e-1669
somite1.81e-1683
paraxial mesoderm1.81e-1683
presomitic mesoderm1.81e-1683
presumptive segmental plate1.81e-1683
trunk paraxial mesoderm1.81e-1683
presumptive paraxial mesoderm1.81e-1683
circulatory system4.70e-15113
blood vessel7.74e-1560
epithelial tube open at both ends7.74e-1560
blood vasculature7.74e-1560
vascular cord7.74e-1560
cardiovascular system1.16e-14110
multilaminar epithelium1.19e-1482
anatomical system5.43e-14625
anatomical group9.41e-14626
dermomyotome2.21e-1370
adult organism3.01e-13115
tube4.81e-13194
muscle tissue1.32e-1263
musculature1.32e-1263
musculature of body1.32e-1263
skeletal muscle tissue4.10e-1261
striated muscle tissue4.10e-1261
myotome4.10e-1261
multi-tissue structure4.85e-12347
epithelial tube2.87e-11118
unilaminar epithelium7.60e-11138
trunk mesenchyme9.85e-11143
trunk3.41e-10216
artery9.78e-1042
arterial blood vessel9.78e-1042
arterial system9.78e-1042
systemic artery2.24e-0933
systemic arterial system2.24e-0933
embryonic structure3.16e-09605
developing anatomical structure3.16e-09605
germ layer3.34e-09604
embryonic tissue3.34e-09604
presumptive structure3.34e-09604
epiblast (generic)3.34e-09604
embryo6.70e-09612
endothelium1.30e-0818
blood vessel endothelium1.30e-0818
cardiovascular system endothelium1.30e-0818
tissue1.24e-07787
aorta1.68e-0721
aortic system1.68e-0721
squamous epithelium1.89e-0725
adipose tissue2.22e-0714
head3.17e-07123
surface structure3.46e-0795
anterior region of body4.85e-07129
craniocervical region4.85e-07129
primary circulatory organ7.06e-0727
simple squamous epithelium9.07e-0722


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


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.