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Coexpression cluster:C4001: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001637!6.81e-31!42;UBERON:0003509!6.81e-31!42;UBERON:0004572!6.81e-31!42;UBERON:0004573!2.04e-25!33;UBERON:0004571!2.04e-25!33;UBERON:0007500!6.63e-25!59;UBERON:0001981!6.63e-25!59;UBERON:0004537!6.63e-25!59;UBERON:0006965!6.63e-25!59;UBERON:0000055!2.78e-22!68;UBERON:0002329!2.80e-22!71;UBERON:0003059!2.80e-22!71;UBERON:0007282!2.80e-22!71;UBERON:0004290!2.80e-22!71;UBERON:0009618!2.80e-22!71;UBERON:0003077!8.93e-22!72;UBERON:0007285!8.93e-22!72;UBERON:0007524!2.76e-21!73;UBERON:0001134!1.78e-20!62;UBERON:0002036!1.78e-20!62;UBERON:0003082!1.78e-20!62;UBERON:0002049!6.86e-20!78;UBERON:0007798!6.86e-20!78;UBERON:0002385!1.90e-19!64;UBERON:0001015!1.90e-19!64;UBERON:0000383!1.90e-19!64;UBERON:0000486!4.67e-19!83;UBERON:0007503!4.88e-19!78;UBERON:0004872!2.57e-18!83;UBERON:0000490!3.51e-15!148;UBERON:0004535!8.47e-14!109;UBERON:0001009!4.63e-13!112;UBERON:0005256!9.99e-13!122;UBERON:0003914!1.33e-12!117;UBERON:0000947!1.02e-11!21;UBERON:0010191!1.02e-11!21;UBERON:0002097!4.31e-10!41;UBERON:0002199!4.52e-10!46;UBERON:0002416!4.52e-10!46;UBERON:0003104!3.16e-09!160;UBERON:0009142!3.16e-09!160;UBERON:0003102!7.29e-09!99;UBERON:0001758!1.89e-08!6;UBERON:0003672!1.89e-08!6;UBERON:0002204!2.83e-08!167;UBERON:0010260!2.84e-08!9;UBERON:0004237!3.06e-08!10;UBERON:0004695!3.06e-08!10;UBERON:0002111!3.06e-08!10;UBERON:0004178!3.06e-08!10;UBERON:0003834!6.15e-08!5;UBERON:0001533!6.15e-08!5;UBERON:0001135!2.62e-07!15;UBERON:0003129!4.45e-07!7;UBERON:0000926!5.92e-07!315;UBERON:0004120!5.92e-07!315;UBERON:0006603!5.92e-07!315;UBERON:0001310!9.74e-07!4
|ontology_enrichment_uberon=UBERON:0001637!6.81e-31!42;UBERON:0003509!6.81e-31!42;UBERON:0004572!6.81e-31!42;UBERON:0004573!2.04e-25!33;UBERON:0004571!2.04e-25!33;UBERON:0007500!6.63e-25!59;UBERON:0001981!6.63e-25!59;UBERON:0004537!6.63e-25!59;UBERON:0006965!6.63e-25!59;UBERON:0000055!2.78e-22!68;UBERON:0002329!2.80e-22!71;UBERON:0003059!2.80e-22!71;UBERON:0007282!2.80e-22!71;UBERON:0004290!2.80e-22!71;UBERON:0009618!2.80e-22!71;UBERON:0003077!8.93e-22!72;UBERON:0007285!8.93e-22!72;UBERON:0007524!2.76e-21!73;UBERON:0001134!1.78e-20!62;UBERON:0002036!1.78e-20!62;UBERON:0003082!1.78e-20!62;UBERON:0002049!6.86e-20!78;UBERON:0007798!6.86e-20!78;UBERON:0002385!1.90e-19!64;UBERON:0001015!1.90e-19!64;UBERON:0000383!1.90e-19!64;UBERON:0000486!4.67e-19!83;UBERON:0007503!4.88e-19!78;UBERON:0004872!2.57e-18!83;UBERON:0000490!3.51e-15!148;UBERON:0004535!8.47e-14!109;UBERON:0001009!4.63e-13!112;UBERON:0005256!9.99e-13!122;UBERON:0003914!1.33e-12!117;UBERON:0000947!1.02e-11!21;UBERON:0010191!1.02e-11!21;UBERON:0002097!4.31e-10!41;UBERON:0002199!4.52e-10!46;UBERON:0002416!4.52e-10!46;UBERON:0003104!3.16e-09!160;UBERON:0009142!3.16e-09!160;UBERON:0003102!7.29e-09!99;UBERON:0001758!1.89e-08!6;UBERON:0003672!1.89e-08!6;UBERON:0002204!2.83e-08!167;UBERON:0010260!2.84e-08!9;UBERON:0004237!3.06e-08!10;UBERON:0004695!3.06e-08!10;UBERON:0002111!3.06e-08!10;UBERON:0004178!3.06e-08!10;UBERON:0003834!6.15e-08!5;UBERON:0001533!6.15e-08!5;UBERON:0001135!2.62e-07!15;UBERON:0003129!4.45e-07!7;UBERON:0000926!5.92e-07!315;UBERON:0004120!5.92e-07!315;UBERON:0006603!5.92e-07!315;UBERON:0001310!9.74e-07!4
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}}
}}

Revision as of 16:29, 26 November 2012


Full id: C4001_Fibroblast_Smooth_mesenchymal_Mesenchymal_mesothelioma_thyroid_leiomyoma



Phase1 CAGE Peaks

Hg19::chr1:86044170..86044182,-p12@DDAH1
Hg19::chr1:98409165..98409171,+p@chr1:98409165..98409171
+
Hg19::chr6:57127802..57127808,-p@chr6:57127802..57127808
-


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>

Cell Type
Ontology termp-valuen
vascular associated smooth muscle cell1.25e-2432
muscle precursor cell9.35e-2358
myoblast9.35e-2358
multi-potent skeletal muscle stem cell9.35e-2358
fibroblast1.56e-2276
muscle cell1.14e-2155
smooth muscle cell1.65e-2143
smooth muscle myoblast1.65e-2143
contractile cell2.15e-1959
electrically responsive cell2.25e-1861
electrically active cell2.25e-1861
non-terminally differentiated cell2.95e-16106
multi fate stem cell9.14e-16427
somatic cell2.27e-15588
somatic stem cell4.34e-15433
skin fibroblast7.35e-1523
mesodermal cell1.58e-14121
stem cell3.22e-14441
animal cell5.31e-10679
eukaryotic cell5.31e-10679
mesenchymal stem cell of adipose9.63e-098
fibroblast of periodontium1.89e-086
aortic smooth muscle cell3.06e-0810
smooth muscle cell of the subclavian artery6.15e-085
native cell5.52e-07722
smooth muscle cell of the umbilical artery9.74e-074
Uber Anatomy
Ontology termp-valuen
artery6.81e-3142
arterial blood vessel6.81e-3142
arterial system6.81e-3142
systemic artery2.04e-2533
systemic arterial system2.04e-2533
epithelial tube open at both ends6.63e-2559
blood vessel6.63e-2559
blood vasculature6.63e-2559
vascular cord6.63e-2559
vessel2.78e-2268
somite2.80e-2271
presomitic mesoderm2.80e-2271
presumptive segmental plate2.80e-2271
dermomyotome2.80e-2271
trunk paraxial mesoderm2.80e-2271
paraxial mesoderm8.93e-2272
presumptive paraxial mesoderm8.93e-2272
dense mesenchyme tissue2.76e-2173
skeletal muscle tissue1.78e-2062
striated muscle tissue1.78e-2062
myotome1.78e-2062
vasculature6.86e-2078
vascular system6.86e-2078
muscle tissue1.90e-1964
musculature1.90e-1964
musculature of body1.90e-1964
multilaminar epithelium4.67e-1983
epithelial vesicle4.88e-1978
splanchnic layer of lateral plate mesoderm2.57e-1883
unilaminar epithelium3.51e-15148
cardiovascular system8.47e-14109
circulatory system4.63e-13112
trunk mesenchyme9.99e-13122
epithelial tube1.33e-12117
aorta1.02e-1121
aortic system1.02e-1121
skin of body4.31e-1041
integument4.52e-1046
integumental system4.52e-1046
mesenchyme3.16e-09160
entire embryonic mesenchyme3.16e-09160
surface structure7.29e-0999
periodontium1.89e-086
dentition1.89e-086
musculoskeletal system2.83e-08167
umbilical blood vessel2.84e-089
blood vessel smooth muscle3.06e-0810
arterial system smooth muscle3.06e-0810
artery smooth muscle tissue3.06e-0810
aorta smooth muscle tissue3.06e-0810
thoracic segment blood vessel6.15e-085
subclavian artery6.15e-085
smooth muscle tissue2.62e-0715
skull4.45e-077
mesoderm5.92e-07315
mesoderm-derived structure5.92e-07315
presumptive mesoderm5.92e-07315
umbilical artery9.74e-074
Disease
Ontology termp-valuen
ovarian cancer6.84e-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)

{{{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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