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Coexpression cluster:C4105: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000468!8.98e-15!656;UBERON:0003104!5.08e-13!160;UBERON:0009142!5.08e-13!160;UBERON:0003914!7.54e-12!117;UBERON:0004872!1.22e-11!83;UBERON:0005256!1.40e-11!122;UBERON:0000467!1.56e-11!624;UBERON:0000480!2.15e-11!625;UBERON:0002049!4.57e-11!78;UBERON:0007798!4.57e-11!78;UBERON:0000055!6.78e-11!68;UBERON:0000926!1.88e-10!315;UBERON:0004120!1.88e-10!315;UBERON:0006603!1.88e-10!315;UBERON:0007503!4.85e-10!78;UBERON:0007500!5.66e-10!59;UBERON:0001981!5.66e-10!59;UBERON:0004537!5.66e-10!59;UBERON:0006965!5.66e-10!59;UBERON:0003102!5.39e-09!99;UBERON:0007524!1.83e-08!73;UBERON:0000119!2.23e-08!309;UBERON:0003077!2.44e-08!72;UBERON:0007285!2.44e-08!72;UBERON:0000486!2.51e-08!83;UBERON:0001637!2.81e-08!42;UBERON:0003509!2.81e-08!42;UBERON:0004572!2.81e-08!42;UBERON:0002100!3.02e-08!199;UBERON:0000475!3.08e-08!264;UBERON:0002329!3.75e-08!71;UBERON:0003059!3.75e-08!71;UBERON:0007282!3.75e-08!71;UBERON:0004290!3.75e-08!71;UBERON:0009618!3.75e-08!71;UBERON:0000483!4.42e-08!306;UBERON:0005423!5.14e-08!581;UBERON:0004111!5.36e-08!240;UBERON:0000490!8.04e-08!148;UBERON:0001009!9.74e-08!112;UBERON:0002385!1.28e-07!64;UBERON:0001015!1.28e-07!64;UBERON:0000383!1.28e-07!64;UBERON:0002199!1.42e-07!46;UBERON:0002416!1.42e-07!46;UBERON:0000923!1.87e-07!560;UBERON:0010316!1.87e-07!560;UBERON:0005291!1.87e-07!560;UBERON:0006598!1.87e-07!560;UBERON:0010317!1.87e-07!560;UBERON:0002532!1.87e-07!560;UBERON:0002050!1.89e-07!564;UBERON:0004535!2.09e-07!109;UBERON:0000922!2.95e-07!592;UBERON:0001134!3.62e-07!62;UBERON:0002036!3.62e-07!62;UBERON:0003082!3.62e-07!62;UBERON:0000479!4.69e-07!773;UBERON:0003103!7.45e-07!68;UBERON:0000477!9.39e-07!373;UBERON:0000481!9.62e-07!342
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}}
}}

Revision as of 16:33, 26 November 2012


Full id: C4105_Mesenchymal_Adipocyte_Preadipocyte_leiomyoma_Osteoblast_breast_Renal



Phase1 CAGE Peaks

Hg19::chr22:43015363..43015380,-p@chr22:43015363..43015380
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Hg19::chr22:43015486..43015596,-p@chr22:43015486..43015596
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Hg19::chr22:43015698..43015781,-p2@CYB5R3


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>

Cell Type
Ontology termp-valuen
fibroblast3.28e-1276
mesodermal cell1.16e-09121
fat cell8.22e-0815
preadipocyte1.30e-0712
contractile cell2.57e-0759
Uber Anatomy
Ontology termp-valuen
multi-cellular organism8.98e-15656
mesenchyme5.08e-13160
entire embryonic mesenchyme5.08e-13160
epithelial tube7.54e-12117
splanchnic layer of lateral plate mesoderm1.22e-1183
trunk mesenchyme1.40e-11122
anatomical system1.56e-11624
anatomical group2.15e-11625
vasculature4.57e-1178
vascular system4.57e-1178
vessel6.78e-1168
mesoderm1.88e-10315
mesoderm-derived structure1.88e-10315
presumptive mesoderm1.88e-10315
epithelial vesicle4.85e-1078
epithelial tube open at both ends5.66e-1059
blood vessel5.66e-1059
blood vasculature5.66e-1059
vascular cord5.66e-1059
surface structure5.39e-0999
dense mesenchyme tissue1.83e-0873
cell layer2.23e-08309
paraxial mesoderm2.44e-0872
presumptive paraxial mesoderm2.44e-0872
multilaminar epithelium2.51e-0883
artery2.81e-0842
arterial blood vessel2.81e-0842
arterial system2.81e-0842
trunk3.02e-08199
organism subdivision3.08e-08264
somite3.75e-0871
presomitic mesoderm3.75e-0871
presumptive segmental plate3.75e-0871
dermomyotome3.75e-0871
trunk paraxial mesoderm3.75e-0871
epithelium4.42e-08306
developing anatomical structure5.14e-08581
anatomical conduit5.36e-08240
unilaminar epithelium8.04e-08148
circulatory system9.74e-08112
muscle tissue1.28e-0764
musculature1.28e-0764
musculature of body1.28e-0764
integument1.42e-0746
integumental system1.42e-0746
germ layer1.87e-07560
germ layer / neural crest1.87e-07560
embryonic tissue1.87e-07560
presumptive structure1.87e-07560
germ layer / neural crest derived structure1.87e-07560
epiblast (generic)1.87e-07560
embryonic structure1.89e-07564
cardiovascular system2.09e-07109
embryo2.95e-07592
skeletal muscle tissue3.62e-0762
striated muscle tissue3.62e-0762
myotome3.62e-0762
tissue4.69e-07773
compound organ7.45e-0768
anatomical cluster9.39e-07373
multi-tissue structure9.62e-07342


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.

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