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Coexpression cluster:C2484: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.50e-20!106;DOID:0050687!2.56e-15!143;DOID:1749!2.42e-08!14;DOID:299!8.58e-08!25
|ontology_enrichment_disease=DOID:305!1.50e-20!106;DOID:0050687!2.56e-15!143;DOID:1749!2.42e-08!14;DOID:299!8.58e-08!25
|ontology_enrichment_uberon=UBERON:0004119!2.63e-19!169;UBERON:0000925!2.63e-19!169;UBERON:0006595!2.63e-19!169;UBERON:0000064!2.31e-15!219;UBERON:0000464!8.79e-15!104;UBERON:0001007!9.60e-15!155;UBERON:0001555!9.60e-15!155;UBERON:0007026!9.60e-15!155;UBERON:0004921!2.31e-14!129;UBERON:0004185!2.31e-14!129;UBERON:0001004!3.38e-14!72;UBERON:0000466!7.85e-14!126;UBERON:0000077!5.72e-13!130;UBERON:0000481!1.73e-12!347;UBERON:0000065!5.14e-12!53;UBERON:0001041!8.13e-12!98;UBERON:0005177!4.07e-11!107;UBERON:0000062!6.10e-11!511;UBERON:0001048!6.58e-11!168;UBERON:0008947!3.26e-10!38;UBERON:0003258!3.26e-10!38;UBERON:0000072!1.82e-09!46;UBERON:0005157!3.06e-09!51;UBERON:0001008!5.29e-09!45;UBERON:0006554!6.18e-09!44;UBERON:0005911!7.12e-09!82;UBERON:0000063!9.29e-09!97;UBERON:0002553!1.14e-08!70;UBERON:0009569!1.24e-08!113;UBERON:0000475!4.81e-08!365;UBERON:0005153!8.76e-08!37;UBERON:0005156!1.38e-07!59;UBERON:0000990!1.38e-07!59;UBERON:0003064!1.58e-07!37;UBERON:0003104!1.67e-07!238;UBERON:0009142!1.67e-07!238;UBERON:0003886!2.13e-07!63;UBERON:0005181!2.39e-07!35;UBERON:0005178!2.87e-07!34;UBERON:0002224!2.87e-07!34;UBERON:0007023!5.38e-07!115;UBERON:0003103!7.14e-07!69
|ontology_enrichment_uberon=UBERON:0004119!2.63e-19!169;UBERON:0000925!2.63e-19!169;UBERON:0006595!2.63e-19!169;UBERON:0000064!2.31e-15!219;UBERON:0000464!8.79e-15!104;UBERON:0001007!9.60e-15!155;UBERON:0001555!9.60e-15!155;UBERON:0007026!9.60e-15!155;UBERON:0004921!2.31e-14!129;UBERON:0004185!2.31e-14!129;UBERON:0001004!3.38e-14!72;UBERON:0000466!7.85e-14!126;UBERON:0000077!5.72e-13!130;UBERON:0000481!1.73e-12!347;UBERON:0000065!5.14e-12!53;UBERON:0001041!8.13e-12!98;UBERON:0005177!4.07e-11!107;UBERON:0000062!6.10e-11!511;UBERON:0001048!6.58e-11!168;UBERON:0008947!3.26e-10!38;UBERON:0003258!3.26e-10!38;UBERON:0000072!1.82e-09!46;UBERON:0005157!3.06e-09!51;UBERON:0001008!5.29e-09!45;UBERON:0006554!6.18e-09!44;UBERON:0005911!7.12e-09!82;UBERON:0000063!9.29e-09!97;UBERON:0002553!1.14e-08!70;UBERON:0009569!1.24e-08!113;UBERON:0000475!4.81e-08!365;UBERON:0005153!8.76e-08!37;UBERON:0005156!1.38e-07!59;UBERON:0000990!1.38e-07!59;UBERON:0003064!1.58e-07!37;UBERON:0003104!1.67e-07!238;UBERON:0009142!1.67e-07!238;UBERON:0003886!2.13e-07!63;UBERON:0005181!2.39e-07!35;UBERON:0005178!2.87e-07!34;UBERON:0002224!2.87e-07!34;UBERON:0007023!5.38e-07!115;UBERON:0003103!7.14e-07!69
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}}
}}

Revision as of 11:40, 5 September 2012


Full id: C2484_Alveolar_Mallassezderived_Urothelial_epidermoid_Esophageal_Corneal_endometrial



Phase1 CAGE Peaks

Hg19::chr19:36001122..36001196,-p6@DMKN
Hg19::chr19:36001304..36001382,-p1@DMKN
Hg19::chr19:36001386..36001429,-p4@DMKN
Hg19::chr19:36001433..36001463,-p7@DMKN


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 cell1.05e-32254
endo-epithelial cell7.16e-1443
endodermal cell4.44e-1059
respiratory epithelial cell4.21e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.63e-19169
endoderm2.63e-19169
presumptive endoderm2.63e-19169
organ part2.31e-15219
anatomical space8.79e-15104
digestive system9.60e-15155
digestive tract9.60e-15155
primitive gut9.60e-15155
subdivision of digestive tract2.31e-14129
endodermal part of digestive tract2.31e-14129
respiratory system3.38e-1472
immaterial anatomical entity7.85e-14126
mixed endoderm/mesoderm-derived structure5.72e-13130
multi-tissue structure1.73e-12347
respiratory tract5.14e-1253
foregut8.13e-1298
trunk region element4.07e-11107
organ6.10e-11511
primordium6.58e-11168
respiratory primordium3.26e-1038
endoderm of foregut3.26e-1038
segment of respiratory tract1.82e-0946
epithelial fold3.06e-0951
renal system5.29e-0945
urinary system structure6.18e-0944
endo-epithelium7.12e-0982
organ segment9.29e-0997
anatomical cavity1.14e-0870
subdivision of trunk1.24e-08113
organism subdivision4.81e-08365
epithelial bud8.76e-0837
reproductive structure1.38e-0759
reproductive system1.38e-0759
intermediate mesoderm1.58e-0737
mesenchyme1.67e-07238
entire embryonic mesenchyme1.67e-07238
body cavity precursor2.13e-0763
thoracic segment organ2.39e-0735
thoracic cavity element2.87e-0734
thoracic cavity2.87e-0734
adult organism5.38e-07115
compound organ7.14e-0769
Disease
Ontology termp-valuen
carcinoma1.50e-20106
cell type cancer2.56e-15143
squamous cell carcinoma2.42e-0814
adenocarcinoma8.58e-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
CEBPB#105147.971147625824820.0002476385788090830.00268150601682133
CTBP2#1488462.71700033932816.45042639894877e-083.95581962818444e-06
CTCF#1066445.360256373075030.001211145381643620.00817335309598593
CTCFL#140690419.74647435897446.5732084880439e-060.000192945284227885
EGR1#195844.988179094810140.001615011500076050.0101449648776881
HEY1#2346244.040111043105710.00375304636917980.0186073776288046
NANOG#79923429.24477848101271.36586687657858e-065.33270170927068e-05
PAX5#507946.669565531177830.0005052774169483260.00443861284789858
RAD21#5885410.35503389545638.6948481184721e-050.00129393166521104
RXRA#6256420.07461713913336.1537798808435e-060.000182221326049167
SMC3#9126415.04493284493281.95092670935632e-050.000437989756230578
SP1#666745.69838137814090.0009482606065333980.00684182310782325
STAT1#6772420.70658749719925.43610708103893e-060.000165329524588417
STAT3#6774410.51946499715428.16377768286615e-050.0012315712515107
TAF1#687243.343046285745290.008005664898701650.0322260025575449
TAF7#6879411.43306940492395.85061525419808e-050.000969123563097848
TBP#690843.706770687096390.005296377814784350.0244247981012171
TCF12#6938410.63446490218647.8163066689251e-050.00120065782055577
ZBTB7A#5134147.35190930787590.000342223540015990.0034653368524074
ZEB1#6935416.88843201754391.22862303393937e-050.000304210908111887
ZNF143#7702413.50087655222793.00867915035614e-050.000620994944237243
ZNF263#1012748.221841637010680.0002187871180958320.00248909671316019



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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