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Coexpression cluster:C2136: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2136_Alveolar_serous_Placental_Renal_amniotic_Small_Mammary
|full_id=C2136_Alveolar_serous_Placental_Renal_amniotic_Small_Mammary
|id=C2136
|id=C2136

Revision as of 14:49, 12 September 2012


Full id: C2136_Alveolar_serous_Placental_Renal_amniotic_Small_Mammary



Phase1 CAGE Peaks

Hg19::chr11:560958..561046,+p1@RASSF7
Hg19::chr11:706174..706213,+p2@EPS8L2
Hg19::chr11:706215..706216,+p6@EPS8L2
Hg19::chr11:706219..706260,+p1@EPS8L2


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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.05e-30169
endoderm3.05e-30169
presumptive endoderm3.05e-30169
digestive system6.92e-24155
digestive tract6.92e-24155
primitive gut6.92e-24155
subdivision of digestive tract2.45e-22129
endodermal part of digestive tract2.45e-22129
mixed endoderm/mesoderm-derived structure1.03e-19130
immaterial anatomical entity5.76e-19126
trunk region element2.67e-17107
subdivision of trunk5.75e-16113
foregut1.05e-1598
mesenchyme5.77e-15238
entire embryonic mesenchyme5.77e-15238
endo-epithelium6.63e-1582
anatomical space3.65e-14104
multi-tissue structure8.54e-14347
renal system1.88e-1345
urinary system structure2.53e-1344
respiratory system1.36e-1272
primordium3.40e-12168
abdomen element3.09e-1155
abdominal segment element3.09e-1155
trunk9.16e-11216
abdominal segment of trunk2.84e-1061
abdomen2.84e-1061
respiratory tract4.14e-1053
gut epithelium9.50e-1054
duct1.45e-0926
organ part1.50e-09219
organism subdivision1.90e-09365
gland2.11e-0959
kidney2.24e-0927
kidney mesenchyme2.24e-0927
kidney rudiment2.24e-0927
kidney field2.24e-0927
reproductive structure3.50e-0959
reproductive system3.50e-0959
exocrine gland3.86e-0931
exocrine system3.86e-0931
intermediate mesoderm3.97e-0937
extraembryonic membrane8.58e-0914
membranous layer8.58e-0914
cavitated compound organ1.19e-0832
respiratory primordium2.00e-0838
endoderm of foregut2.00e-0838
anatomical cavity2.56e-0870
organ2.58e-08511
organ segment3.54e-0897
female organism7.63e-0841
orifice1.04e-0735
epithelial bud1.17e-0737
segment of respiratory tract1.61e-0746
urogenital ridge1.79e-0720
reproductive organ2.21e-0748
mesonephros2.48e-0718
pronephros2.48e-0718
nephrogenic cord2.48e-0718
pronephric mesoderm2.48e-0718
rostral part of nephrogenic cord2.48e-0718
presumptive pronephric mesoderm2.48e-0718
thoracic cavity element5.05e-0734
thoracic cavity5.05e-0734
excretory tube5.14e-0717
mesonephric epithelium5.14e-0717
mesonephric tubule5.14e-0717
nephric duct5.14e-0717
kidney epithelium5.14e-0717
renal duct5.14e-0717
mesonephric duct5.14e-0717
pronephric duct5.14e-0717
sac5.32e-0726
epithelium of foregut-midgut junction7.01e-0725
anatomical boundary7.01e-0725
hepatobiliary system7.01e-0725
foregut-midgut junction7.01e-0725
septum transversum7.01e-0725
epithelial sac7.10e-0725
internal genitalia8.22e-0725
nephron epithelium9.14e-0716
nephron9.14e-0716
uriniferous tubule9.14e-0716
metanephric mesenchyme9.14e-0716
nephrogenic mesenchyme9.14e-0716
Disease
Ontology termp-valuen
carcinoma1.34e-21106
cell type cancer2.76e-14143
adenocarcinoma4.17e-0825


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
E2F1#186944.907389214879320.001724022357361790.0106252313808868
E2F6#187645.017155731697390.00157802193473060.00994971219761706
EGR1#195844.988179094810140.001615011500076050.0101260842922761
HEY1#2346244.040111043105710.00375304636917980.0185545282722258



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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