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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2462_cervical_small_colon_clear_embryonic_renal_mucinous
|full_id=C2462_cervical_small_colon_clear_embryonic_renal_mucinous
|id=C2462
|id=C2462

Revision as of 15:12, 12 September 2012


Full id: C2462_cervical_small_colon_clear_embryonic_renal_mucinous



Phase1 CAGE Peaks

Hg19::chr18:47376135..47376153,-p6@MYO5B
Hg19::chr18:47376159..47376168,-p7@MYO5B
Hg19::chr18:47376170..47376195,-p5@MYO5B
Hg19::chr18:47376197..47376227,-p2@MYO5B


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
epithelial cell3.23e-60254
endo-epithelial cell9.76e-1643
embryonic cell1.54e-15248
endodermal cell3.00e-1559
squamous epithelial cell6.75e-1362
epithelial cell of lung4.66e-0919
respiratory epithelial cell1.64e-0713
kidney cell2.56e-0718
kidney epithelial cell2.56e-0718
mesothelial cell6.00e-0719
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.24e-23169
endoderm5.24e-23169
presumptive endoderm5.24e-23169
digestive system3.15e-20155
digestive tract3.15e-20155
primitive gut3.15e-20155
subdivision of digestive tract2.96e-18129
endodermal part of digestive tract2.96e-18129
respiratory primordium1.00e-1538
endoderm of foregut1.00e-1538
respiratory tract3.23e-1553
mixed endoderm/mesoderm-derived structure5.48e-15130
endo-epithelium1.09e-1382
multi-tissue structure2.40e-13347
segment of respiratory tract5.00e-1346
organ segment7.93e-1397
respiratory system9.41e-1372
foregut1.39e-1298
trunk region element1.58e-12107
mesenchyme8.89e-12238
entire embryonic mesenchyme8.89e-12238
primordium1.60e-11168
epithelial bud2.72e-1137
immaterial anatomical entity3.48e-11126
anatomical system5.14e-11625
anatomical group7.39e-11626
embryo1.29e-10612
anatomical space1.79e-10104
multi-cellular organism2.27e-10659
organ part3.62e-10219
embryonic structure4.37e-10605
developing anatomical structure4.37e-10605
germ layer7.29e-10604
embryonic tissue7.29e-10604
presumptive structure7.29e-10604
epiblast (generic)7.29e-10604
lung1.52e-0922
respiratory tube1.52e-0922
respiration organ1.52e-0922
pair of lungs1.52e-0922
lung primordium1.52e-0922
lung bud1.52e-0922
urinary system structure3.49e-0944
thoracic cavity element3.54e-0934
thoracic cavity3.54e-0934
subdivision of trunk4.21e-09113
respiratory tract epithelium4.66e-0919
lung epithelium4.66e-0919
renal system1.07e-0845
thoracic segment organ1.32e-0835
epithelial fold4.00e-0851
respiratory system epithelium4.06e-0828
organ4.18e-08511
epithelium1.30e-07309
larynx1.31e-079
cell layer1.34e-07312
duct2.91e-0726
kidney3.25e-0727
kidney mesenchyme3.25e-0727
kidney rudiment3.25e-0727
kidney field3.25e-0727
trunk4.78e-07216
Disease
Ontology termp-valuen
carcinoma3.81e-34106
cell type cancer3.56e-28143
cancer5.23e-18235
disease of cellular proliferation1.32e-17239
adenocarcinoma1.94e-0925
squamous cell carcinoma3.88e-0714
respiratory system cancer4.76e-0716
lung cancer6.08e-0715


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
CEBPB#105147.971147625824820.0002476385788090830.00268067221519919
CTCF#1066445.360256373075030.001211145381643620.00817282499925556
E2F1#186944.907389214879320.001724022357361790.0106497409937013
ESR1#2099430.76860329615451.11467714392546e-064.6050540440835e-05
FOS#235348.99795530889440.0001525147711168630.00194843916583169
FOSL2#2355416.93020060456171.2165416097647e-050.000303739873732287
GTF2F1#2962412.73966087675773.79492332235515e-050.00071800361750625
JUN#3725412.51282919233634.07770316866756e-050.000743101101435127
JUND#372746.994663941871030.000417684217818580.00391619732693731
MAX#414946.452555509007120.0005767613195645490.00485346671936201
RAD21#5885410.35503389545638.6948481184721e-050.00129374731820075
RFX5#5993412.04791082719514.74457429336527e-050.00082655311864016
TAF1#687243.343046285745290.008005664898701650.0322173102788033
TBP#690843.706770687096390.005296377814784350.0244172509313262
TCF7L2#6934410.77017656313737.42969445082454e-050.00115468728980605
ZNF263#1012748.221841637010680.0002187871180958320.00248801261180429



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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