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Coexpression cluster:C3192: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.16e-33!106;DOID:0050687!8.47e-31!143;DOID:162!3.66e-22!235;DOID:14566!7.07e-21!239;DOID:299!6.38e-11!25;DOID:1749!7.51e-08!14;DOID:3095!2.46e-07!22;DOID:2994!2.46e-07!22
|ontology_enrichment_disease=DOID:305!1.16e-33!106;DOID:0050687!8.47e-31!143;DOID:162!3.66e-22!235;DOID:14566!7.07e-21!239;DOID:299!6.38e-11!25;DOID:1749!7.51e-08!14;DOID:3095!2.46e-07!22;DOID:2994!2.46e-07!22
|ontology_enrichment_uberon=UBERON:0004119!3.41e-18!169;UBERON:0000925!3.41e-18!169;UBERON:0006595!3.41e-18!169;UBERON:0001007!1.76e-15!155;UBERON:0001555!1.76e-15!155;UBERON:0007026!1.76e-15!155;UBERON:0004921!5.10e-15!129;UBERON:0004185!5.10e-15!129;UBERON:0001004!5.70e-15!72;UBERON:0000065!1.62e-13!53;UBERON:0000077!3.40e-13!130;UBERON:0008947!9.08e-13!38;UBERON:0003258!9.08e-13!38;UBERON:0001041!6.02e-12!98;UBERON:0000464!3.99e-11!104;UBERON:0000072!5.49e-11!46;UBERON:0005153!3.19e-09!37;UBERON:0005177!4.02e-09!107;UBERON:0000063!5.18e-09!97;UBERON:0000064!9.84e-09!219;UBERON:0005181!1.79e-08!35;UBERON:0000466!2.33e-08!126;UBERON:0005178!3.62e-08!34;UBERON:0002224!3.62e-08!34;UBERON:0005409!4.83e-08!35;UBERON:0002048!1.00e-07!22;UBERON:0000117!1.00e-07!22;UBERON:0000171!1.00e-07!22;UBERON:0000170!1.00e-07!22;UBERON:0005597!1.00e-07!22;UBERON:0000118!1.00e-07!22;UBERON:0005157!3.38e-07!51;UBERON:0005911!5.28e-07!82;UBERON:0004802!6.82e-07!19;UBERON:0000115!6.82e-07!19
|ontology_enrichment_uberon=UBERON:0004119!3.41e-18!169;UBERON:0000925!3.41e-18!169;UBERON:0006595!3.41e-18!169;UBERON:0001007!1.76e-15!155;UBERON:0001555!1.76e-15!155;UBERON:0007026!1.76e-15!155;UBERON:0004921!5.10e-15!129;UBERON:0004185!5.10e-15!129;UBERON:0001004!5.70e-15!72;UBERON:0000065!1.62e-13!53;UBERON:0000077!3.40e-13!130;UBERON:0008947!9.08e-13!38;UBERON:0003258!9.08e-13!38;UBERON:0001041!6.02e-12!98;UBERON:0000464!3.99e-11!104;UBERON:0000072!5.49e-11!46;UBERON:0005153!3.19e-09!37;UBERON:0005177!4.02e-09!107;UBERON:0000063!5.18e-09!97;UBERON:0000064!9.84e-09!219;UBERON:0005181!1.79e-08!35;UBERON:0000466!2.33e-08!126;UBERON:0005178!3.62e-08!34;UBERON:0002224!3.62e-08!34;UBERON:0005409!4.83e-08!35;UBERON:0002048!1.00e-07!22;UBERON:0000117!1.00e-07!22;UBERON:0000171!1.00e-07!22;UBERON:0000170!1.00e-07!22;UBERON:0005597!1.00e-07!22;UBERON:0000118!1.00e-07!22;UBERON:0005157!3.38e-07!51;UBERON:0005911!5.28e-07!82;UBERON:0004802!6.82e-07!19;UBERON:0000115!6.82e-07!19
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}}
}}

Revision as of 14:06, 5 September 2012


Full id: C3192_choriocarcinoma_rectal_breast_pancreatic_adenocarcinoma_Alveolar_Renal



Phase1 CAGE Peaks

Hg19::chr11:66139068..66139120,-p2@SLC29A2
Hg19::chr11:66139128..66139152,-p3@SLC29A2
Hg19::chr11:66139160..66139170,-p9@SLC29A2


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 cell8.73e-29254
endo-epithelial cell5.80e-1343
endodermal cell4.18e-1059
epithelial cell of lung6.82e-0719
germ line cell7.54e-077
germ cell7.54e-077
epithelial cell of alimentary canal8.98e-0721
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.41e-18169
endoderm3.41e-18169
presumptive endoderm3.41e-18169
digestive system1.76e-15155
digestive tract1.76e-15155
primitive gut1.76e-15155
subdivision of digestive tract5.10e-15129
endodermal part of digestive tract5.10e-15129
respiratory system5.70e-1572
respiratory tract1.62e-1353
mixed endoderm/mesoderm-derived structure3.40e-13130
respiratory primordium9.08e-1338
endoderm of foregut9.08e-1338
foregut6.02e-1298
anatomical space3.99e-11104
segment of respiratory tract5.49e-1146
epithelial bud3.19e-0937
trunk region element4.02e-09107
organ segment5.18e-0997
organ part9.84e-09219
thoracic segment organ1.79e-0835
immaterial anatomical entity2.33e-08126
thoracic cavity element3.62e-0834
thoracic cavity3.62e-0834
gastrointestinal system4.83e-0835
lung1.00e-0722
respiratory tube1.00e-0722
respiration organ1.00e-0722
pair of lungs1.00e-0722
lung primordium1.00e-0722
lung bud1.00e-0722
epithelial fold3.38e-0751
endo-epithelium5.28e-0782
respiratory tract epithelium6.82e-0719
lung epithelium6.82e-0719
Disease
Ontology termp-valuen
carcinoma1.16e-33106
cell type cancer8.47e-31143
cancer3.66e-22235
disease of cellular proliferation7.07e-21239
adenocarcinoma6.38e-1125
squamous cell carcinoma7.51e-0814
germ cell and embryonal cancer2.46e-0722
germ cell cancer2.46e-0722


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#90536.336201576962630.003930750035764890.0189259878744756
E2F1#186934.907389214879320.008460985347239390.0323826168528413
EGR1#195834.988179094810140.008056488137383440.0319236470228095
ELK4#2005316.2356816584680.0002336043955745990.00255069623308056
ESR1#2099220.51240219743630.003099741577095180.0163024428729098
HMGN3#932438.178547723350590.001827766942164210.0108374106774548
IRF1#365937.63716375356390.002244692747297240.0127673165142673
MAX#414936.452555509007120.003721913834265510.0185853673888049
MXI1#460139.96157162875930.001011470541259020.00718472229195069
SIN3A#2594235.408884726815140.006318961977991520.0275563100763897
SMARCC2#6601394.15537442689761.19621075407887e-064.8460455758434e-05
SP1#666735.69838137814090.005403962701712170.0245555369215157
TFAP2A#7020316.5186343730450.0002218033880766340.00247435633917278
TFAP2C#7022310.80922860986020.0007916746575753130.00613183844278464
YY1#752834.911170749853860.008441455341808260.0328116846344528
ZBTB7A#5134137.35190930787590.002516255860282270.0139673263774658
ZEB1#6935316.88843201754390.0002075486917327580.00242083737054696



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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