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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2933_testicular_rectal_squamous_malignant_nasal_small_large
|full_id=C2933_testicular_rectal_squamous_malignant_nasal_small_large
|id=C2933
|id=C2933

Revision as of 15:44, 12 September 2012


Full id: C2933_testicular_rectal_squamous_malignant_nasal_small_large



Phase1 CAGE Peaks

Hg19::chr8:95653327..95653364,+p3@ESRP1
Hg19::chr8:95653373..95653415,+p1@ESRP1
Hg19::chr8:95653432..95653460,+p2@ESRP1
Hg19::chr8:95653478..95653491,+p4@ESRP1


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 structure7.52e-24169
endoderm7.52e-24169
presumptive endoderm7.52e-24169
digestive system7.86e-18155
digestive tract7.86e-18155
primitive gut7.86e-18155
respiratory system5.02e-1672
anatomical space1.03e-15104
subdivision of digestive tract1.89e-15129
endodermal part of digestive tract1.89e-15129
mixed endoderm/mesoderm-derived structure7.37e-15130
immaterial anatomical entity1.18e-13126
epithelial bud1.22e-1337
endo-epithelium2.46e-1282
thoracic segment organ4.17e-1135
epithelial fold5.71e-1151
respiratory tract6.60e-1153
thoracic cavity element8.76e-1134
thoracic cavity8.76e-1134
orifice1.15e-1035
lung1.09e-0922
respiratory tube1.09e-0922
respiration organ1.09e-0922
pair of lungs1.09e-0922
lung primordium1.09e-0922
lung bud1.09e-0922
reproductive structure1.85e-0959
reproductive system1.85e-0959
foregut5.61e-0998
thoracic segment of trunk8.89e-0952
respiratory system epithelium2.28e-0828
respiratory tract epithelium3.67e-0819
lung epithelium3.67e-0819
male organism4.91e-0822
male reproductive system4.91e-0822
reproductive organ9.71e-0848
oral opening1.05e-0721
respiratory primordium1.38e-0738
endoderm of foregut1.38e-0738
mucosa1.65e-0712
extraembryonic membrane3.31e-0714
membranous layer3.31e-0714
segment of respiratory tract3.49e-0746
anatomical cavity4.15e-0770
trunk region element4.32e-07107
male reproductive organ6.08e-0711
organ6.54e-07511
Disease
Ontology termp-valuen
carcinoma2.76e-24106
cell type cancer2.52e-16143
squamous cell carcinoma1.01e-1314
adenocarcinoma3.47e-0725


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
ATF3#467422.46317452600873.92475754624726e-060.000127654236490974
CTCF#1066445.360256373075030.001211145381643620.00820516427824846
EP300#203346.77394172622320.0004748459821442640.00435671084328954
GATA3#2625427.2365163572061.81561517799785e-066.80132832047766e-05
HDAC2#3066413.41562023662633.0859005065161e-050.00062897806986736
JUND#372746.994663941871030.000417684217818580.00392854124862704
MAX#414946.452555509007120.0005767613195645490.00486837270298245
MYC#460945.22228187160940.001344309395272740.00890230986829556
NANOG#79923429.24477848101271.36586687657858e-065.35271184701653e-05
SIN3A#2594245.408884726815140.001168172384885160.00798499611918456
SP1#666745.69838137814090.0009482606065333980.0068607820911494
TAF1#687243.343046285745290.008005664898701650.0323519438305023
TBP#690843.706770687096390.005296377814784350.0245179026904066
TCF12#6938410.63446490218647.8163066689251e-050.00120331257693967
TCF7L2#6934410.77017656313737.42969445082454e-050.00115865291735055
USF1#739146.361499277207960.0006105011399140830.00509388260377782
USF2#7392412.99219738506963.50833029870167e-050.000683594231466611
YY1#752844.911170749853860.00171871838055440.0107132932824065
ZEB1#6935416.88843201754391.22862303393937e-050.000305441944874063



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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