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Coexpression cluster:C2879: Difference between revisions

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|full_id=C2879_salivary_Fibroblast_vagina_liver_Hepatocyte_Skeletal_hepatoblastoma
|full_id=C2879_salivary_Fibroblast_vagina_liver_Hepatocyte_Skeletal_hepatoblastoma
|id=C2879
|id=C2879
|ontology_enrichment_celltype=CL:0000055!1.81e-07!180
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!7.84e-26!347;UBERON:0000475!4.41e-24!365;UBERON:0000468!6.61e-17!659;UBERON:0004119!1.29e-15!169;UBERON:0000925!1.29e-15!169;UBERON:0006595!1.29e-15!169;UBERON:0003104!1.74e-15!238;UBERON:0009142!1.74e-15!238;UBERON:0000922!4.77e-14!612;UBERON:0000467!1.01e-13!625;UBERON:0001007!1.07e-13!155;UBERON:0001555!1.07e-13!155;UBERON:0007026!1.07e-13!155;UBERON:0000480!1.98e-13!626;UBERON:0000062!2.22e-13!511;UBERON:0002050!2.87e-13!605;UBERON:0005423!2.87e-13!605;UBERON:0000119!3.69e-13!312;UBERON:0000923!5.25e-13!604;UBERON:0005291!5.25e-13!604;UBERON:0006598!5.25e-13!604;UBERON:0002532!5.25e-13!604;UBERON:0000483!1.14e-12!309;UBERON:0002100!5.61e-12!216;UBERON:0000924!2.28e-11!173;UBERON:0006601!2.28e-11!173;UBERON:0004121!2.54e-11!169;UBERON:0000477!5.42e-11!286;UBERON:0000077!6.06e-11!130;UBERON:0003102!1.26e-10!95;UBERON:0004921!2.00e-10!129;UBERON:0004185!2.00e-10!129;UBERON:0005256!2.90e-10!143;UBERON:0001048!1.05e-09!168;UBERON:0000064!1.68e-09!219;UBERON:0002530!2.00e-08!59;UBERON:0007023!2.99e-08!115;UBERON:0000033!5.14e-08!123;UBERON:0000161!8.20e-08!35;UBERON:0000153!1.68e-07!129;UBERON:0007811!1.68e-07!129;UBERON:0004111!3.92e-07!241;UBERON:0005177!6.99e-07!107
|ontology_enrichment_uberon=UBERON:0000481!1.41e-25!342;UBERON:0011216!3.91e-17!223;UBERON:0000477!6.39e-17!373;UBERON:0000468!8.08e-16!656;UBERON:0004119!3.10e-15!160;UBERON:0000925!3.10e-15!160;UBERON:0006595!3.10e-15!160;UBERON:0000475!6.09e-14!264;UBERON:0000467!1.61e-13!624;UBERON:0000480!3.11e-13!625;UBERON:0000119!3.72e-13!309;UBERON:0001007!6.90e-13!145;UBERON:0001555!6.90e-13!145;UBERON:0007026!6.90e-13!145;UBERON:0000483!1.17e-12!306;UBERON:0000062!4.62e-12!503;UBERON:0004121!8.96e-12!171;UBERON:0000924!8.96e-12!171;UBERON:0006601!8.96e-12!171;UBERON:0003102!9.82e-12!99;UBERON:0003104!1.09e-11!160;UBERON:0009142!1.09e-11!160;UBERON:0000922!3.12e-11!592;UBERON:0005423!1.79e-10!581;UBERON:0000064!1.03e-09!218;UBERON:0001048!1.33e-09!160;UBERON:0004921!1.38e-09!118;UBERON:0002050!1.52e-09!564;UBERON:0002100!2.73e-09!199;UBERON:0005256!3.41e-09!122;UBERON:0000923!6.00e-09!560;UBERON:0010316!6.00e-09!560;UBERON:0005291!6.00e-09!560;UBERON:0006598!6.00e-09!560;UBERON:0010317!6.00e-09!560;UBERON:0002532!6.00e-09!560;UBERON:0002530!1.43e-08!59;UBERON:0007023!2.61e-08!114;UBERON:0010314!2.64e-08!132;UBERON:0000161!7.74e-08!36;UBERON:0004923!7.79e-07!66;UBERON:0002365!7.90e-07!31;UBERON:0002330!7.90e-07!31;UBERON:0010371!8.55e-07!104
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268651973950782!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435288681902614!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00107344358415519!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.4550249062561e-05!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000724428212708722!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000719306709371053!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000628610031207402!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.01866052890982!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486522699733478!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142761624050451!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00889892431595927!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000444649506869647!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129930067627001!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000828626412416012!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000242182123905179!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00685698189335606!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323319271599189!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245016124467693!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115761578211199!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000231060936351236!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509062902606682!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000683084466939044!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107088192904618!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249944299133785
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}}
}}

Revision as of 14:31, 19 October 2012


Full id: C2879_salivary_Fibroblast_vagina_liver_Hepatocyte_Skeletal_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr7:134576184..134576236,+p2@CALD1
Hg19::chr7:134576237..134576280,+p5@CALD1
Hg19::chr7:134576283..134576309,+p9@CALD1
Hg19::chr7:134576317..134576374,+p3@CALD1


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.41e-25342
organ system subdivision3.91e-17223
anatomical cluster6.39e-17373
multi-cellular organism8.08e-16656
endoderm-derived structure3.10e-15160
endoderm3.10e-15160
presumptive endoderm3.10e-15160
organism subdivision6.09e-14264
anatomical system1.61e-13624
anatomical group3.11e-13625
cell layer3.72e-13309
digestive system6.90e-13145
digestive tract6.90e-13145
primitive gut6.90e-13145
epithelium1.17e-12306
organ4.62e-12503
ectoderm-derived structure8.96e-12171
ectoderm8.96e-12171
presumptive ectoderm8.96e-12171
surface structure9.82e-1299
mesenchyme1.09e-11160
entire embryonic mesenchyme1.09e-11160
embryo3.12e-11592
developing anatomical structure1.79e-10581
organ part1.03e-09218
primordium1.33e-09160
subdivision of digestive tract1.38e-09118
embryonic structure1.52e-09564
trunk2.73e-09199
trunk mesenchyme3.41e-09122
germ layer6.00e-09560
germ layer / neural crest6.00e-09560
embryonic tissue6.00e-09560
presumptive structure6.00e-09560
germ layer / neural crest derived structure6.00e-09560
epiblast (generic)6.00e-09560
gland1.43e-0859
adult organism2.61e-08114
structure with developmental contribution from neural crest2.64e-08132
orifice7.74e-0836
organ component layer7.79e-0766
exocrine gland7.90e-0731
exocrine system7.90e-0731
ecto-epithelium8.55e-07104


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#105147.971147625824820.0002476385788090830.00268651973950782
EP300#203346.77394172622320.0004748459821442640.00435288681902614
FOXA1#3169411.08141974938556.62943068949433e-050.00107344358415519
FOXA2#3170424.63046375266522.71504128667089e-069.4550249062561e-05
GATA2#2624412.7449317335543.78864877853583e-050.000724428212708722
GTF2F1#2962412.73966087675773.79492332235515e-050.000719306709371053
HDAC2#3066413.41562023662633.0859005065161e-050.000628610031207402
HEY1#2346244.040111043105710.00375304636917980.01866052890982
MAX#414946.452555509007120.0005767613195645490.00486522699733478
MXI1#460149.96157162875930.0001015224754950450.00142761624050451
MYC#460945.22228187160940.001344309395272740.00889892431595927
NR3C1#2908414.9730233311731.98868032687801e-050.000444649506869647
RAD21#5885410.35503389545638.6948481184721e-050.00129930067627001
RFX5#5993412.04791082719514.74457429336527e-050.000828626412416012
SMARCB1#6598418.25271578115749.00423392720929e-060.000242182123905179
SP1#666745.69838137814090.0009482606065333980.00685698189335606
TAF1#687243.343046285745290.008005664898701650.0323319271599189
TBP#690843.706770687096390.005296377814784350.0245016124467693
TCF7L2#6934410.77017656313737.42969445082454e-050.00115761578211199
TRIM28#10155418.59052504526258.36730015875654e-060.000231060936351236
USF1#739146.361499277207960.0006105011399140830.00509062902606682
USF2#7392412.99219738506963.50833029870167e-050.000683084466939044
YY1#752844.911170749853860.00171871838055440.0107088192904618
ZNF263#1012748.221841637010680.0002187871180958320.00249944299133785



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.