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Coexpression cluster:C2019: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2019_mature_sacrococcigeal_gastric_Adipocyte_Synoviocyte_Mesenchymal_Chondrocyte
|full_id=C2019_mature_sacrococcigeal_gastric_Adipocyte_Synoviocyte_Mesenchymal_Chondrocyte
|id=C2019
|id=C2019

Revision as of 14:41, 12 September 2012


Full id: C2019_mature_sacrococcigeal_gastric_Adipocyte_Synoviocyte_Mesenchymal_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr9:129884902..129884922,-p1@ANGPTL2
Hg19::chr9:129884924..129884937,-p3@ANGPTL2
Hg19::chr9:129884944..129884979,-p2@ANGPTL2
Hg19::chr9:129884994..129885007,-p4@ANGPTL2
Hg19::chr9:129885010..129885017,-p5@ANGPTL2


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
organism subdivision3.12e-15365
multi-cellular organism6.16e-12659
epithelium9.97e-12309
cell layer1.22e-11312
adult organism1.30e-10115
multi-tissue structure3.08e-10347
splanchnic layer of lateral plate mesoderm4.51e-1084
anatomical cluster5.70e-10286
somite2.12e-0983
paraxial mesoderm2.12e-0983
presomitic mesoderm2.12e-0983
presumptive segmental plate2.12e-0983
trunk paraxial mesoderm2.12e-0983
presumptive paraxial mesoderm2.12e-0983
muscle tissue2.48e-0963
musculature2.48e-0963
musculature of body2.48e-0963
anatomical conduit4.41e-09241
dermomyotome8.15e-0970
skeletal muscle tissue1.04e-0861
striated muscle tissue1.04e-0861
myotome1.04e-0861
anatomical system2.88e-08625
anatomical group4.57e-08626
vasculature6.17e-0879
vascular system6.17e-0879
trunk mesenchyme8.47e-08143
primary circulatory organ8.50e-0827
unilaminar epithelium1.08e-07138
adipose tissue1.65e-0714
epithelial tube2.06e-07118
multilaminar epithelium2.43e-0782
tube3.56e-07194
vessel6.45e-0769
surface structure7.67e-0795
blood vessel8.20e-0760
epithelial tube open at both ends8.20e-0760
blood vasculature8.20e-0760
vascular cord8.20e-0760


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
CTCF#1066455.360256373075030.0002259278299937090.00250325447026447
E2F6#187655.017155731697390.0003144978599297790.00323349497865782
HEY1#2346254.040111043105710.0009288852205177990.00675146798981547
MAX#414956.452555509007128.93743970843928e-050.00130859002622976
MYC#460955.22228187160940.0002573944848850610.00276877357162539
PAX5#507956.669565531177837.57493746384605e-050.00117185438273829
SPI1#668858.204323508522732.68916109982495e-050.000575873069724457
TAF1#687253.343046285745290.002394600090870310.0135586684136842
TAF7#6879511.43306940492395.11611886715123e-060.000157617208957642
TBP#690853.706770687096390.001428755106721120.00920585813997454
TCF7L2#6934510.77017656313736.89693748574565e-060.000200308468874802
TFAP2A#7020516.5186343730458.12390055913032e-073.54555808815299e-05
TFAP2C#7022510.80922860986026.77323239348459e-060.000197594865347245
ZNF263#1012758.221841637010682.6606316672286e-050.000572817379290225



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.