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Coexpression cluster:C2918: Difference between revisions

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|full_id=C2918_Mast_mesothelioma_spindle_mesodermal_myxofibrosarcoma_lens_neurofibroma
|full_id=C2918_Mast_mesothelioma_spindle_mesodermal_myxofibrosarcoma_lens_neurofibroma
|id=C2918
|id=C2918
|ontology_enrichment_celltype=CL:0000055!1.14e-23!180;CL:0000057!5.36e-21!75;CL:0000222!5.85e-20!119;CL:0002139!4.33e-12!24;CL:0000115!1.58e-11!35;CL:0000183!8.83e-11!59;CL:0000680!8.83e-11!57;CL:0000056!8.83e-11!57;CL:0000355!8.83e-11!57;CL:0000220!1.54e-10!246;CL:0000071!4.41e-10!18;CL:0002546!4.41e-10!18;CL:0002620!4.89e-10!23;CL:0002321!5.42e-10!248;CL:0000187!6.03e-10!54;CL:0002078!1.20e-09!44;CL:0000213!2.07e-09!57;CL:0000215!2.07e-09!57;CL:0000192!2.35e-08!42;CL:0000514!2.35e-08!42;CL:0000359!3.73e-08!32;CL:0000393!3.24e-07!60;CL:0000211!3.24e-07!60
|ontology_enrichment_celltype=CL:0000057!1.15e-21!76;CL:0000222!8.82e-21!121;CL:0000115!4.50e-12!36;CL:0002139!5.01e-12!24;CL:0000680!5.04e-11!58;CL:0000056!5.04e-11!58;CL:0000355!5.04e-11!58;CL:0000183!8.89e-11!59;CL:0002321!2.31e-10!250;CL:0002078!2.63e-10!45;CL:0000187!2.88e-10!55;CL:0002620!3.17e-10!23;CL:0000071!3.18e-10!18;CL:0002546!3.18e-10!18;CL:0000213!7.95e-10!58;CL:0000215!7.95e-10!58;CL:0000192!9.71e-09!43;CL:0000514!9.71e-09!43;CL:0000359!2.15e-08!32;CL:0000393!1.80e-07!61;CL:0000211!1.80e-07!61
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000119!6.81e-24!312;UBERON:0002049!9.16e-24!79;UBERON:0007798!9.16e-24!79;UBERON:0003914!1.06e-22!118;UBERON:0000483!1.18e-22!309;UBERON:0000475!1.94e-22!365;UBERON:0000477!6.27e-21!286;UBERON:0004111!2.77e-20!241;UBERON:0000055!8.05e-20!69;UBERON:0000025!1.50e-18!194;UBERON:0001981!1.08e-17!60;UBERON:0007500!1.08e-17!60;UBERON:0004537!1.08e-17!60;UBERON:0006965!1.08e-17!60;UBERON:0005256!2.43e-17!143;UBERON:0004872!2.67e-17!84;UBERON:0000490!1.43e-16!138;UBERON:0001009!3.66e-16!113;UBERON:0004535!4.97e-16!110;UBERON:0000468!3.17e-14!659;UBERON:0001637!3.34e-14!42;UBERON:0003509!3.34e-14!42;UBERON:0004572!3.34e-14!42;UBERON:0000481!3.35e-14!347;UBERON:0002100!3.76e-14!216;UBERON:0000914!5.88e-14!83;UBERON:0002329!5.88e-14!83;UBERON:0003077!5.88e-14!83;UBERON:0003059!5.88e-14!83;UBERON:0007282!5.88e-14!83;UBERON:0009618!5.88e-14!83;UBERON:0007285!5.88e-14!83;UBERON:0000467!3.44e-13!625;UBERON:0000480!6.27e-13!626;UBERON:0004290!6.41e-13!70;UBERON:0000486!3.01e-11!82;UBERON:0004573!9.73e-11!33;UBERON:0004571!9.73e-11!33;UBERON:0001986!4.41e-10!18;UBERON:0004638!4.41e-10!18;UBERON:0004852!4.41e-10!18;UBERON:0001134!4.58e-10!61;UBERON:0002036!4.58e-10!61;UBERON:0003082!4.58e-10!61;UBERON:0002385!9.08e-10!63;UBERON:0001015!9.08e-10!63;UBERON:0000383!9.08e-10!63;UBERON:0003102!2.20e-09!95;UBERON:0000487!4.50e-09!22;UBERON:0000947!8.80e-09!21;UBERON:0010191!8.80e-09!21;UBERON:0002199!1.20e-08!45;UBERON:0002416!1.20e-08!45;UBERON:0003104!2.65e-08!238;UBERON:0009142!2.65e-08!238;UBERON:0006914!2.87e-08!25;UBERON:0000923!3.09e-07!604;UBERON:0005291!3.09e-07!604;UBERON:0006598!3.09e-07!604;UBERON:0002532!3.09e-07!604;UBERON:0002050!3.60e-07!605;UBERON:0005423!3.60e-07!605;UBERON:0002097!4.05e-07!40
|ontology_enrichment_uberon=UBERON:0000119!2.44e-24!309;UBERON:0002049!2.45e-23!78;UBERON:0007798!2.45e-23!78;UBERON:0003914!4.20e-23!117;UBERON:0000483!4.39e-23!306;UBERON:0004111!4.50e-20!240;UBERON:0000055!3.16e-19!68;UBERON:0000490!6.23e-19!148;UBERON:0000025!7.78e-19!192;UBERON:0007500!2.85e-17!59;UBERON:0001981!2.85e-17!59;UBERON:0004537!2.85e-17!59;UBERON:0006965!2.85e-17!59;UBERON:0004872!6.28e-17!83;UBERON:0001009!3.36e-16!112;UBERON:0004535!4.31e-16!109;UBERON:0000477!8.87e-16!373;UBERON:0007503!1.10e-15!78;UBERON:0005256!3.41e-15!122;UBERON:0001637!2.02e-14!42;UBERON:0003509!2.02e-14!42;UBERON:0004572!2.02e-14!42;UBERON:0003104!2.25e-14!160;UBERON:0009142!2.25e-14!160;UBERON:0000468!3.54e-14!656;UBERON:0000467!6.90e-14!624;UBERON:0000481!7.61e-14!342;UBERON:0000475!9.82e-14!264;UBERON:0000480!1.25e-13!625;UBERON:0007524!2.94e-13!73;UBERON:0002329!5.67e-13!71;UBERON:0003059!5.67e-13!71;UBERON:0007282!5.67e-13!71;UBERON:0004290!5.67e-13!71;UBERON:0009618!5.67e-13!71;UBERON:0003077!6.96e-13!72;UBERON:0007285!6.96e-13!72;UBERON:0002100!1.41e-12!199;UBERON:0000486!2.10e-11!83;UBERON:0004573!8.81e-11!33;UBERON:0004571!8.81e-11!33;UBERON:0004638!3.18e-10!18;UBERON:0001986!3.18e-10!18;UBERON:0004852!3.18e-10!18;UBERON:0001134!4.03e-10!62;UBERON:0002036!4.03e-10!62;UBERON:0003082!4.03e-10!62;UBERON:0002385!7.67e-10!64;UBERON:0001015!7.67e-10!64;UBERON:0000383!7.67e-10!64;UBERON:0000487!5.73e-09!22;UBERON:0000947!9.48e-09!21;UBERON:0010191!9.48e-09!21;UBERON:0002199!2.12e-08!46;UBERON:0002416!2.12e-08!46;UBERON:0006914!3.15e-08!25;UBERON:0003102!7.26e-08!99;UBERON:0010314!7.99e-08!132;UBERON:0002097!4.44e-07!41;UBERON:0000923!4.60e-07!560;UBERON:0010316!4.60e-07!560;UBERON:0005291!4.60e-07!560;UBERON:0006598!4.60e-07!560;UBERON:0010317!4.60e-07!560;UBERON:0002532!4.60e-07!560;UBERON:0005423!8.02e-07!581
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.0026881951493859!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129391927327857!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106838646520209!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161302944480083!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435594550102458!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195561573734488!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000304467743067854!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.0010737765381205!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000628855342439093!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186685278029515!HNF4A#3172;4:23.1322903629537:3.48990320893214e-06:0.000115892528215473!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000745572901317352!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392748014988338!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.0013006033266186!REST#5978;4:9.65002871612802:0.000115282561421917:0.0015761219311878!RXRA#6256;4:20.0746171391333:6.1537798808435e-06:0.000182635583113218!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00685888146587309!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323419323980931!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245124702028832!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115813411753681!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509266202487915!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00250081075044441
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}}
}}

Revision as of 14:34, 19 October 2012


Full id: C2918_Mast_mesothelioma_spindle_mesodermal_myxofibrosarcoma_lens_neurofibroma



Phase1 CAGE Peaks

Hg19::chr8:13133974..13133985,-p13@DLC1
Hg19::chr8:13134001..13134011,-p14@DLC1
Hg19::chr8:13134015..13134038,-p2@DLC1
Hg19::chr8:13134045..13134063,-p5@DLC1


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><br>


Uber Anatomy
Ontology termp-valuen
cell layer2.44e-24309
vasculature2.45e-2378
vascular system2.45e-2378
epithelial tube4.20e-23117
epithelium4.39e-23306
anatomical conduit4.50e-20240
vessel3.16e-1968
unilaminar epithelium6.23e-19148
tube7.78e-19192
epithelial tube open at both ends2.85e-1759
blood vessel2.85e-1759
blood vasculature2.85e-1759
vascular cord2.85e-1759
splanchnic layer of lateral plate mesoderm6.28e-1783
circulatory system3.36e-16112
cardiovascular system4.31e-16109
anatomical cluster8.87e-16373
epithelial vesicle1.10e-1578
trunk mesenchyme3.41e-15122
artery2.02e-1442
arterial blood vessel2.02e-1442
arterial system2.02e-1442
mesenchyme2.25e-14160
entire embryonic mesenchyme2.25e-14160
multi-cellular organism3.54e-14656
anatomical system6.90e-14624
multi-tissue structure7.61e-14342
organism subdivision9.82e-14264
anatomical group1.25e-13625
dense mesenchyme tissue2.94e-1373
somite5.67e-1371
presomitic mesoderm5.67e-1371
presumptive segmental plate5.67e-1371
dermomyotome5.67e-1371
trunk paraxial mesoderm5.67e-1371
paraxial mesoderm6.96e-1372
presumptive paraxial mesoderm6.96e-1372
trunk1.41e-12199
multilaminar epithelium2.10e-1183
systemic artery8.81e-1133
systemic arterial system8.81e-1133
blood vessel endothelium3.18e-1018
endothelium3.18e-1018
cardiovascular system endothelium3.18e-1018
skeletal muscle tissue4.03e-1062
striated muscle tissue4.03e-1062
myotome4.03e-1062
muscle tissue7.67e-1064
musculature7.67e-1064
musculature of body7.67e-1064
simple squamous epithelium5.73e-0922
aorta9.48e-0921
aortic system9.48e-0921
integument2.12e-0846
integumental system2.12e-0846
squamous epithelium3.15e-0825
surface structure7.26e-0899
structure with developmental contribution from neural crest7.99e-08132
skin of body4.44e-0741
germ layer4.60e-07560
germ layer / neural crest4.60e-07560
embryonic tissue4.60e-07560
presumptive structure4.60e-07560
germ layer / neural crest derived structure4.60e-07560
epiblast (generic)4.60e-07560
developing anatomical structure8.02e-07581


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#105147.971147625824820.0002476385788090830.0026881951493859
CHD2#1106410.34402283411698.73193255208051e-050.00129391927327857
E2F1#186944.907389214879320.001724022357361790.0106838646520209
ELF1#199744.258097958807540.003041525565781240.0161302944480083
EP300#203346.77394172622320.0004748459821442640.00435594550102458
FOS#235348.99795530889440.0001525147711168630.00195561573734488
FOSL2#2355416.93020060456171.2165416097647e-050.000304467743067854
FOXA1#3169411.08141974938556.62943068949433e-050.0010737765381205
HDAC2#3066413.41562023662633.0859005065161e-050.000628855342439093
HEY1#2346244.040111043105710.00375304636917980.0186685278029515
HNF4A#3172423.13229036295373.48990320893214e-060.000115892528215473
JUN#3725412.51282919233634.07770316866756e-050.000745572901317352
JUND#372746.994663941871030.000417684217818580.00392748014988338
RAD21#5885410.35503389545638.6948481184721e-050.0013006033266186
REST#597849.650028716128020.0001152825614219170.0015761219311878
RXRA#6256420.07461713913336.1537798808435e-060.000182635583113218
SP1#666745.69838137814090.0009482606065333980.00685888146587309
TAF1#687243.343046285745290.008005664898701650.0323419323980931
TBP#690843.706770687096390.005296377814784350.0245124702028832
TCF7L2#6934410.77017656313737.42969445082454e-050.00115813411753681
USF1#739146.361499277207960.0006105011399140830.00509266202487915
ZNF263#1012748.221841637010680.0002187871180958320.00250081075044441



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.