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Coexpression cluster:C2462: Difference between revisions

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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
|ontology_enrichment_celltype=CL:0000066!3.23e-60!254;CL:0002076!9.76e-16!43;CL:0000220!1.04e-15!246;CL:0002321!1.54e-15!248;CL:0000223!3.00e-15!59;CL:0000076!6.75e-13!62;CL:0000082!4.66e-09!19;CL:0002368!1.64e-07!13;CL:1000497!2.56e-07!18;CL:0002518!2.56e-07!18;CL:0000077!6.00e-07!19
|ontology_enrichment_celltype=CL:0000066!3.46e-65!253;CL:0002076!6.38e-18!42;CL:0000223!2.34e-16!58;CL:0002321!1.59e-14!250;CL:0000076!4.32e-14!63;CL:0000082!6.24e-11!19;CL:0002368!6.12e-09!13;CL:0000077!6.18e-08!19;CL:1000497!1.35e-07!17;CL:0002518!1.35e-07!17;CL:0002202!5.66e-07!9;CL:0002632!5.66e-07!9
|ontology_enrichment_disease=DOID:305!3.81e-34!106;DOID:0050687!3.56e-28!143;DOID:162!5.23e-18!235;DOID:14566!1.32e-17!239;DOID:299!1.94e-09!25;DOID:1749!3.88e-07!14;DOID:0050615!4.76e-07!16;DOID:1324!6.08e-07!15
|ontology_enrichment_disease=DOID:305!1.19e-35!106;DOID:0050687!1.29e-28!143;DOID:162!2.64e-19!235;DOID:14566!4.10e-19!239;DOID:299!5.87e-09!25;DOID:1749!1.06e-08!14;DOID:0050615!2.15e-08!16;DOID:1324!2.59e-08!15
|ontology_enrichment_uberon=UBERON:0004119!5.24e-23!169;UBERON:0000925!5.24e-23!169;UBERON:0006595!5.24e-23!169;UBERON:0001007!3.15e-20!155;UBERON:0001555!3.15e-20!155;UBERON:0007026!3.15e-20!155;UBERON:0004921!2.96e-18!129;UBERON:0004185!2.96e-18!129;UBERON:0008947!1.00e-15!38;UBERON:0003258!1.00e-15!38;UBERON:0000065!3.23e-15!53;UBERON:0000077!5.48e-15!130;UBERON:0005911!1.09e-13!82;UBERON:0000481!2.40e-13!347;UBERON:0000072!5.00e-13!46;UBERON:0000063!7.93e-13!97;UBERON:0001004!9.41e-13!72;UBERON:0001041!1.39e-12!98;UBERON:0005177!1.58e-12!107;UBERON:0003104!8.89e-12!238;UBERON:0009142!8.89e-12!238;UBERON:0001048!1.60e-11!168;UBERON:0005153!2.72e-11!37;UBERON:0000466!3.48e-11!126;UBERON:0000467!5.14e-11!625;UBERON:0000480!7.39e-11!626;UBERON:0000922!1.29e-10!612;UBERON:0000464!1.79e-10!104;UBERON:0000468!2.27e-10!659;UBERON:0000064!3.62e-10!219;UBERON:0002050!4.37e-10!605;UBERON:0005423!4.37e-10!605;UBERON:0000923!7.29e-10!604;UBERON:0005291!7.29e-10!604;UBERON:0006598!7.29e-10!604;UBERON:0002532!7.29e-10!604;UBERON:0002048!1.52e-09!22;UBERON:0000117!1.52e-09!22;UBERON:0000171!1.52e-09!22;UBERON:0000170!1.52e-09!22;UBERON:0005597!1.52e-09!22;UBERON:0000118!1.52e-09!22;UBERON:0006554!3.49e-09!44;UBERON:0005178!3.54e-09!34;UBERON:0002224!3.54e-09!34;UBERON:0009569!4.21e-09!113;UBERON:0004802!4.66e-09!19;UBERON:0000115!4.66e-09!19;UBERON:0001008!1.07e-08!45;UBERON:0005181!1.32e-08!35;UBERON:0005157!4.00e-08!51;UBERON:0004807!4.06e-08!28;UBERON:0000062!4.18e-08!511;UBERON:0000483!1.30e-07!309;UBERON:0001737!1.31e-07!9;UBERON:0000119!1.34e-07!312;UBERON:0000058!2.91e-07!26;UBERON:0002113!3.25e-07!27;UBERON:0003918!3.25e-07!27;UBERON:0005095!3.25e-07!27;UBERON:0007687!3.25e-07!27;UBERON:0002100!4.78e-07!216
|ontology_enrichment_uberon=UBERON:0004119!5.68e-23!160;UBERON:0000925!5.68e-23!160;UBERON:0006595!5.68e-23!160;UBERON:0001007!6.82e-21!145;UBERON:0001555!6.82e-21!145;UBERON:0007026!6.82e-21!145;UBERON:0004921!3.28e-19!118;UBERON:0008947!5.17e-19!38;UBERON:0003258!5.17e-19!38;UBERON:0000065!4.45e-18!54;UBERON:0001004!2.76e-15!74;UBERON:0000072!3.10e-15!47;UBERON:0000063!5.52e-15!98;UBERON:0005911!9.79e-15!82;UBERON:0005153!8.54e-14!37;UBERON:0001041!4.63e-13!87;UBERON:0000064!7.14e-12!218;UBERON:0005177!9.66e-12!101;UBERON:0002048!1.10e-11!22;UBERON:0000117!1.10e-11!22;UBERON:0000171!1.10e-11!22;UBERON:0000170!1.10e-11!22;UBERON:0005597!1.10e-11!22;UBERON:0000118!1.10e-11!22;UBERON:0000477!1.96e-11!373;UBERON:0001048!3.30e-11!160;UBERON:0000481!5.56e-11!342;UBERON:0004802!6.24e-11!19;UBERON:0000115!6.24e-11!19;UBERON:0005157!9.73e-11!47;UBERON:0005178!4.29e-10!34;UBERON:0002224!4.29e-10!34;UBERON:0004807!4.68e-10!28;UBERON:0005181!1.50e-09!35;UBERON:0006554!1.10e-08!47;UBERON:0000475!1.60e-08!264;UBERON:0001737!2.30e-08!9;UBERON:0001008!2.68e-08!48;UBERON:0009569!4.69e-08!112;UBERON:0011216!2.74e-07!223;UBERON:0005409!4.10e-07!25;UBERON:0002113!4.19e-07!26;UBERON:0003918!4.19e-07!26;UBERON:0011143!4.19e-07!26;UBERON:0005095!4.19e-07!26;UBERON:0007687!4.19e-07!26;UBERON:0000062!5.45e-07!503
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268067221519919!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817282499925556!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106497409937013!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.6050540440835e-05!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00194843916583169!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000303739873732287!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.00071800361750625!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000743101101435127!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391619732693731!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485346671936201!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129374731820075!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.00082655311864016!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322173102788033!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244172509313262!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115468728980605!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248801261180429
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268067221519919!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817282499925556!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106497409937013!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.6050540440835e-05!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00194843916583169!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000303739873732287!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.00071800361750625!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000743101101435127!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391619732693731!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485346671936201!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129374731820075!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.00082655311864016!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322173102788033!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244172509313262!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115468728980605!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248801261180429
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}}
}}

Revision as of 14:03, 19 October 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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.68e-23160
endoderm5.68e-23160
presumptive endoderm5.68e-23160
digestive system6.82e-21145
digestive tract6.82e-21145
primitive gut6.82e-21145
subdivision of digestive tract3.28e-19118
respiratory primordium5.17e-1938
endoderm of foregut5.17e-1938
respiratory tract4.45e-1854
respiratory system2.76e-1574
segment of respiratory tract3.10e-1547
organ segment5.52e-1598
endo-epithelium9.79e-1582
epithelial bud8.54e-1437
foregut4.63e-1387
organ part7.14e-12218
trunk region element9.66e-12101
lung1.10e-1122
respiratory tube1.10e-1122
respiration organ1.10e-1122
pair of lungs1.10e-1122
lung primordium1.10e-1122
lung bud1.10e-1122
anatomical cluster1.96e-11373
primordium3.30e-11160
multi-tissue structure5.56e-11342
respiratory tract epithelium6.24e-1119
lung epithelium6.24e-1119
epithelial fold9.73e-1147
thoracic cavity element4.29e-1034
thoracic cavity4.29e-1034
respiratory system epithelium4.68e-1028
thoracic segment organ1.50e-0935
urinary system structure1.10e-0847
organism subdivision1.60e-08264
larynx2.30e-089
renal system2.68e-0848
subdivision of trunk4.69e-08112
organ system subdivision2.74e-07223
gastrointestinal system4.10e-0725
kidney4.19e-0726
kidney mesenchyme4.19e-0726
upper urinary tract4.19e-0726
kidney rudiment4.19e-0726
kidney field4.19e-0726
organ5.45e-07503
Disease
Ontology termp-valuen
carcinoma1.19e-35106
cell type cancer1.29e-28143
cancer2.64e-19235
disease of cellular proliferation4.10e-19239
adenocarcinoma5.87e-0925
squamous cell carcinoma1.06e-0814
respiratory system cancer2.15e-0816
lung cancer2.59e-0815


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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