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Coexpression cluster:C1641: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!1.08e-25!83;UBERON:0002329!1.08e-25!83;UBERON:0003077!1.08e-25!83;UBERON:0003059!1.08e-25!83;UBERON:0007282!1.08e-25!83;UBERON:0009618!1.08e-25!83;UBERON:0007285!1.08e-25!83;UBERON:0004290!1.22e-22!70;UBERON:0000475!1.34e-19!365;UBERON:0001134!3.93e-19!61;UBERON:0002036!3.93e-19!61;UBERON:0003082!3.93e-19!61;UBERON:0002385!4.21e-19!63;UBERON:0001015!4.21e-19!63;UBERON:0000383!4.21e-19!63;UBERON:0000486!1.17e-18!82;UBERON:0005256!2.80e-17!143;UBERON:0000468!2.81e-16!659;UBERON:0000481!5.03e-15!347;UBERON:0003102!1.64e-12!95;UBERON:0002100!1.42e-11!216;UBERON:0000467!4.61e-11!625;UBERON:0000480!8.42e-11!626;UBERON:0002199!1.99e-10!45;UBERON:0002416!1.99e-10!45;UBERON:0000119!2.08e-10!312;UBERON:0000479!6.44e-10!787;UBERON:0003104!6.60e-10!238;UBERON:0009142!6.60e-10!238;UBERON:0000922!9.11e-10!612;UBERON:0000483!9.48e-10!309;UBERON:0000490!9.82e-10!138;UBERON:0002050!5.23e-09!605;UBERON:0005423!5.23e-09!605;UBERON:0004872!7.56e-09!84;UBERON:0000923!8.87e-09!604;UBERON:0005291!8.87e-09!604;UBERON:0006598!8.87e-09!604;UBERON:0002532!8.87e-09!604;UBERON:0002097!1.35e-08!40;UBERON:0002049!7.90e-07!79;UBERON:0007798!7.90e-07!79
|ontology_enrichment_uberon=UBERON:0000914!1.08e-25!83;UBERON:0002329!1.08e-25!83;UBERON:0003077!1.08e-25!83;UBERON:0003059!1.08e-25!83;UBERON:0007282!1.08e-25!83;UBERON:0009618!1.08e-25!83;UBERON:0007285!1.08e-25!83;UBERON:0004290!1.22e-22!70;UBERON:0000475!1.34e-19!365;UBERON:0001134!3.93e-19!61;UBERON:0002036!3.93e-19!61;UBERON:0003082!3.93e-19!61;UBERON:0002385!4.21e-19!63;UBERON:0001015!4.21e-19!63;UBERON:0000383!4.21e-19!63;UBERON:0000486!1.17e-18!82;UBERON:0005256!2.80e-17!143;UBERON:0000468!2.81e-16!659;UBERON:0000481!5.03e-15!347;UBERON:0003102!1.64e-12!95;UBERON:0002100!1.42e-11!216;UBERON:0000467!4.61e-11!625;UBERON:0000480!8.42e-11!626;UBERON:0002199!1.99e-10!45;UBERON:0002416!1.99e-10!45;UBERON:0000119!2.08e-10!312;UBERON:0000479!6.44e-10!787;UBERON:0003104!6.60e-10!238;UBERON:0009142!6.60e-10!238;UBERON:0000922!9.11e-10!612;UBERON:0000483!9.48e-10!309;UBERON:0000490!9.82e-10!138;UBERON:0002050!5.23e-09!605;UBERON:0005423!5.23e-09!605;UBERON:0004872!7.56e-09!84;UBERON:0000923!8.87e-09!604;UBERON:0005291!8.87e-09!604;UBERON:0006598!8.87e-09!604;UBERON:0002532!8.87e-09!604;UBERON:0002097!1.35e-08!40;UBERON:0002049!7.90e-07!79;UBERON:0007798!7.90e-07!79
|tf_chipseq_enrich=RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318856325953844!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356891559586411!TAL1#6886;2:11.9474466709761:0.010475778180992:0.0388012837338945
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}}
}}

Revision as of 14:14, 5 September 2012


Full id: C1641_Mesenchymal_Nucleus_Fibroblast_tenocyte_Pericytes_normal_Smooth



Phase1 CAGE Peaks

Hg19::chr11:66103136..66103189,-p2@RIN1
Hg19::chr7:100199967..100200012,+p1@PCOLCE
Hg19::chr7:100200018..100200030,+p2@PCOLCE
Hg19::chr7:100200840..100200890,+p6@PCOLCE
Hg19::chr7:100201073..100201087,-p2@ENST00000544873


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


GO IDGO nameFDR corrected p-value
GO:0005518collagen binding0.0324298847608999



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
somite1.08e-2583
paraxial mesoderm1.08e-2583
presomitic mesoderm1.08e-2583
presumptive segmental plate1.08e-2583
trunk paraxial mesoderm1.08e-2583
presumptive paraxial mesoderm1.08e-2583
dermomyotome1.22e-2270
organism subdivision1.34e-19365
skeletal muscle tissue3.93e-1961
striated muscle tissue3.93e-1961
myotome3.93e-1961
muscle tissue4.21e-1963
musculature4.21e-1963
musculature of body4.21e-1963
multilaminar epithelium1.17e-1882
trunk mesenchyme2.80e-17143
multi-cellular organism2.81e-16659
multi-tissue structure5.03e-15347
surface structure1.64e-1295
trunk1.42e-11216
anatomical system4.61e-11625
anatomical group8.42e-11626
integument1.99e-1045
integumental system1.99e-1045
cell layer2.08e-10312
tissue6.44e-10787
mesenchyme6.60e-10238
entire embryonic mesenchyme6.60e-10238
embryo9.11e-10612
epithelium9.48e-10309
unilaminar epithelium9.82e-10138
embryonic structure5.23e-09605
developing anatomical structure5.23e-09605
splanchnic layer of lateral plate mesoderm7.56e-0984
germ layer8.87e-09604
embryonic tissue8.87e-09604
presumptive structure8.87e-09604
epiblast (generic)8.87e-09604
skin of body1.35e-0840
vasculature7.90e-0779
vascular system7.90e-0779


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
RAD21#588536.21302033727380.007751055068811640.0318856325953844
REST#597835.790017229676810.009468788694433940.0356891559586411
TAL1#6886211.94744667097610.0104757781809920.0388012837338945



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.