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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2015_small_squamous_amniotic_rectal_malignant_maxillary_oral
|full_id=C2015_small_squamous_amniotic_rectal_malignant_maxillary_oral
|id=C2015
|id=C2015

Revision as of 14:41, 12 September 2012


Full id: C2015_small_squamous_amniotic_rectal_malignant_maxillary_oral



Phase1 CAGE Peaks

Hg19::chr8:82644522..82644557,-p4@ZFAND1
Hg19::chr8:82644562..82644654,-p2@ZFAND1
Hg19::chr8:82644655..82644687,-p3@ZFAND1
Hg19::chr8:82644669..82644738,+p1@CHMP4C
Hg19::chr8:82644741..82644791,+p2@CHMP4C


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 cell1.46e-42254
endodermal cell8.34e-1959
endo-epithelial cell3.69e-1743
epithelial cell of alimentary canal7.03e-0921
respiratory epithelial cell4.43e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.09e-27169
endoderm4.09e-27169
presumptive endoderm4.09e-27169
digestive system7.51e-22155
digestive tract7.51e-22155
primitive gut7.51e-22155
subdivision of digestive tract6.33e-21129
endodermal part of digestive tract6.33e-21129
mixed endoderm/mesoderm-derived structure4.84e-19130
foregut5.73e-1698
immaterial anatomical entity3.06e-14126
respiratory system7.19e-1472
endo-epithelium2.87e-1382
primordium3.61e-13168
organ8.84e-13511
anatomical space9.38e-13104
trunk region element1.39e-11107
respiratory tract3.15e-1153
respiratory primordium2.54e-1038
endoderm of foregut2.54e-1038
multi-tissue structure2.17e-09347
epithelial bud3.18e-0937
organ part1.19e-08219
segment of respiratory tract1.55e-0846
epithelial fold3.27e-0851
gastrointestinal system3.31e-0835
multi-cellular organism4.55e-08659
embryo6.30e-08612
lung2.07e-0722
respiratory tube2.07e-0722
respiration organ2.07e-0722
pair of lungs2.07e-0722
lung primordium2.07e-0722
lung bud2.07e-0722
organ segment2.11e-0797
anatomical cavity2.90e-0770
subdivision of trunk4.99e-07113
mesenchyme5.10e-07238
entire embryonic mesenchyme5.10e-07238
embryonic structure6.47e-07605
developing anatomical structure6.47e-07605
thoracic cavity element8.55e-0734
thoracic cavity8.55e-0734
thoracic segment organ8.89e-0735
mucosa8.97e-0712
germ layer9.16e-07604
embryonic tissue9.16e-07604
presumptive structure9.16e-07604
epiblast (generic)9.16e-07604
Disease
Ontology termp-valuen
carcinoma1.17e-36106
cell type cancer2.04e-28143
cancer9.36e-14235
disease of cellular proliferation5.31e-13239
adenocarcinoma2.63e-1025
squamous cell carcinoma2.34e-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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90556.336201576962639.78880505817628e-050.00139187612181194
E2F1#186954.907389214879320.0003512818099256460.00353580579672557
E2F6#187655.017155731697390.0003144978599297790.0032331766899504
EBF1#187958.9064668465691.78355672307702e-050.000406887026215467
ELF1#199754.258097958807540.0007142416939776840.00573893585761928
FOSL2#2355516.93020060456177.18315284751475e-073.21285353422524e-05
FOXA1#3169511.08141974938555.98116883436141e-060.00017934748546996
FOXA2#3170524.63046375266521.10174651693954e-076.41389657093916e-06
GABPB1#255357.067683836182175.6685482528729e-050.000949811504864098
HEY1#2346254.040111043105710.0009288852205177990.00675099815905765
HMGN3#932458.178547723350592.73180911341838e-050.000582973870037397
MXI1#460159.96157162875931.01894348670516e-050.000266844129408225
MYC#460955.22228187160940.0002573944848850610.00276848842501657
SIN3A#2594255.408884726815140.0002159522671657270.00248390295490323
TAF1#687253.343046285745290.002394600090870310.0135579333671476
TBP#690853.706770687096390.001428755106721120.00920529022768953
TCF7L2#6934510.77017656313736.89693748574565e-060.000200252781227075
USF1#739156.361499277207969.59569864925045e-050.00137113855688749
YY1#752854.911170749853860.00034993140821360.00353242667141118



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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