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Coexpression cluster:C1716: Difference between revisions

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|full_id=C1716_Corneal_oral_Keratinocyte_mesothelioma_Esophageal_Urothelial_anaplastic
|full_id=C1716_Corneal_oral_Keratinocyte_mesothelioma_Esophageal_Urothelial_anaplastic
|id=C1716
|id=C1716
|ontology_enrichment_celltype=CL:0000066!2.21e-51!254;CL:0000220!4.14e-33!246;CL:0002321!4.51e-33!248;CL:0000223!8.92e-18!59;CL:0002076!2.97e-16!43;CL:0000548!1.28e-15!679;CL:0000004!1.28e-15!679;CL:0000255!1.28e-15!679;CL:0000076!1.54e-15!62;CL:0000012!4.40e-15!682;CL:0000222!1.33e-10!119;CL:0000055!5.61e-10!180;CL:0002251!1.07e-08!21;CL:0000213!1.90e-08!57;CL:0000215!1.90e-08!57;CL:0002368!6.98e-08!13;CL:1000449!3.51e-07!16;CL:1000497!3.62e-07!18;CL:0002518!3.62e-07!18;CL:0000063!8.16e-07!578
|ontology_enrichment_celltype=CL:0000066!2.54e-50!253;CL:0002321!1.39e-33!250;CL:0000223!4.37e-18!58;CL:0002076!2.44e-16!42;CL:0000548!5.31e-16!679;CL:0000255!5.31e-16!679;CL:0000076!1.79e-15!63;CL:0000222!7.33e-11!121;CL:0002251!5.73e-09!20;CL:0000213!1.22e-08!58;CL:0000215!1.22e-08!58;CL:0002368!7.13e-08!13;CL:1000497!9.11e-07!17;CL:0002518!9.11e-07!17
|ontology_enrichment_disease=DOID:0050687!1.27e-12!143;DOID:305!2.32e-12!106;DOID:7!7.21e-09!39
|ontology_enrichment_disease=DOID:0050687!3.11e-12!143;DOID:305!4.60e-12!106;DOID:7!5.11e-09!39
|ontology_enrichment_uberon=UBERON:0003104!2.97e-19!238;UBERON:0009142!2.97e-19!238;UBERON:0004119!7.38e-19!169;UBERON:0000925!7.38e-19!169;UBERON:0006595!7.38e-19!169;UBERON:0002100!2.51e-16!216;UBERON:0000481!4.08e-16!347;UBERON:0000475!4.14e-16!365;UBERON:0001007!7.61e-14!155;UBERON:0001555!7.61e-14!155;UBERON:0007026!7.61e-14!155;UBERON:0005256!1.12e-13!143;UBERON:0000490!3.89e-12!138;UBERON:0000119!1.28e-11!312;UBERON:0000468!1.30e-11!659;UBERON:0000483!1.51e-11!309;UBERON:0003102!2.44e-11!95;UBERON:0005911!2.46e-11!82;UBERON:0000077!2.71e-11!130;UBERON:0009569!8.08e-11!113;UBERON:0006554!2.42e-10!44;UBERON:0005177!3.69e-10!107;UBERON:0001008!5.01e-10!45;UBERON:0000466!7.07e-10!126;UBERON:0001048!7.63e-10!168;UBERON:0003914!1.18e-09!118;UBERON:0004921!1.59e-09!129;UBERON:0004185!1.59e-09!129;UBERON:0000467!3.66e-09!625;UBERON:0003929!6.45e-09!54;UBERON:0000480!6.53e-09!626;UBERON:0005172!8.24e-09!55;UBERON:0005173!8.24e-09!55;UBERON:0002417!1.66e-08!61;UBERON:0000916!1.66e-08!61;UBERON:0005085!2.20e-08!29;UBERON:0001444!3.76e-08!48;UBERON:0000477!5.18e-08!286;UBERON:0003064!6.25e-08!37;UBERON:0001041!1.04e-07!98;UBERON:0000058!1.73e-07!26;UBERON:0004211!3.51e-07!16;UBERON:0001285!3.51e-07!16;UBERON:0007684!3.51e-07!16;UBERON:0003220!3.51e-07!16;UBERON:0004208!3.51e-07!16;UBERON:0002530!3.73e-07!59;UBERON:0001004!4.53e-07!72;UBERON:0002365!6.07e-07!31;UBERON:0002330!6.07e-07!31;UBERON:0002097!8.39e-07!40;UBERON:0000064!8.52e-07!219
|ontology_enrichment_uberon=UBERON:0000475!1.28e-21!264;UBERON:0004119!1.61e-18!160;UBERON:0000925!1.61e-18!160;UBERON:0006595!1.61e-18!160;UBERON:0002100!1.21e-14!199;UBERON:0001007!1.85e-13!145;UBERON:0001555!1.85e-13!145;UBERON:0007026!1.85e-13!145;UBERON:0000481!2.66e-13!342;UBERON:0003104!9.03e-13!160;UBERON:0009142!9.03e-13!160;UBERON:0000490!1.73e-12!148;UBERON:0000477!3.91e-12!373;UBERON:0003102!6.73e-12!99;UBERON:0000119!3.29e-11!309;UBERON:0005911!3.45e-11!82;UBERON:0000483!3.53e-11!306;UBERON:0006554!3.67e-11!47;UBERON:0000468!5.47e-11!656;UBERON:0001008!7.79e-11!48;UBERON:0005177!1.50e-10!101;UBERON:0009569!3.86e-10!112;UBERON:0000467!3.00e-09!624;UBERON:0005256!4.52e-09!122;UBERON:0003914!4.72e-09!117;UBERON:0000480!5.18e-09!625;UBERON:0004921!5.28e-09!118;UBERON:0001048!5.29e-09!160;UBERON:0003929!9.32e-09!54;UBERON:0005172!2.51e-08!54;UBERON:0005173!2.51e-08!54;UBERON:0000033!5.33e-08!56;UBERON:0002417!5.65e-08!60;UBERON:0000916!5.65e-08!60;UBERON:0001444!8.65e-08!49;UBERON:0005085!1.32e-07!31;UBERON:0000466!1.78e-07!117;UBERON:0001004!2.05e-07!74;UBERON:0001041!2.56e-07!87;UBERON:0002530!2.71e-07!59;UBERON:0002365!5.26e-07!31;UBERON:0002330!5.26e-07!31;UBERON:0000153!8.37e-07!62;UBERON:0007811!8.37e-07!62
|tf_chipseq_enrich=CCNT2#905;5:6.33620157696263:9.78880505817628e-05:0.00138979474098814!CHD2#1106;5:10.3440228341169:8.43981772346334e-06:0.000230142590919266!CTBP2#1488;5:62.7170003393281:1.02712351233917e-09:9.50148383571214e-08!CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249663280464638!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352493475661266!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00322650707202418!EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330638186762853!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00572835879875099!HDAC2#3066;4:10.732496189301:0.000145096579747875:0.00188549728658558!IRF1#3659;5:7.6371637535639:3.84754333311872e-05:0.000723763649437295!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000983709389562028!MXI1#4601;5:9.9615716287593:1.01894348670516e-05:0.000266509989501628!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276336581074331!RFX5#5993;5:12.0479108271951:3.93714721313598e-06:0.000127461784808651!SMARCB1#6598;5:18.2527157811574:4.93125075403021e-07:2.31467369662994e-05!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204156458711173!SRF#6722;5:13.7971782621678:1.9987012616697e-06:7.31915712017959e-05!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135264015842071!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00918263105174445!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000199697603014635!TRIM28#10155;5:18.5905250452625:4.49912775886781e-07:2.13583820003816e-05!ZBTB7A#51341;5:7.3519093078759:4.65425347594289e-05:0.000815443010860592!ZNF263#10127;5:8.22184163701068:2.6606316672286e-05:0.000570816989921299
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}}
}}

Revision as of 11:36, 19 October 2012


Full id: C1716_Corneal_oral_Keratinocyte_mesothelioma_Esophageal_Urothelial_anaplastic



Phase1 CAGE Peaks

Hg19::chr14:23451697..23451713,-p4@AJUBA
Hg19::chr14:23451725..23451742,-p1@AJUBA
Hg19::chr14:23451753..23451767,-p2@AJUBA
Hg19::chr14:23451797..23451814,-p3@AJUBA
Hg19::chr14:23451816..23451828,-p5@AJUBA


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 cell2.54e-50253
embryonic cell1.39e-33250
endodermal cell4.37e-1858
endo-epithelial cell2.44e-1642
animal cell5.31e-16679
eukaryotic cell5.31e-16679
squamous epithelial cell1.79e-1563
mesodermal cell7.33e-11121
epithelial cell of alimentary canal5.73e-0920
lining cell1.22e-0858
barrier cell1.22e-0858
respiratory epithelial cell7.13e-0813
kidney cell9.11e-0717
kidney epithelial cell9.11e-0717
Uber Anatomy
Ontology termp-valuen
organism subdivision1.28e-21264
endoderm-derived structure1.61e-18160
endoderm1.61e-18160
presumptive endoderm1.61e-18160
trunk1.21e-14199
digestive system1.85e-13145
digestive tract1.85e-13145
primitive gut1.85e-13145
multi-tissue structure2.66e-13342
mesenchyme9.03e-13160
entire embryonic mesenchyme9.03e-13160
unilaminar epithelium1.73e-12148
anatomical cluster3.91e-12373
surface structure6.73e-1299
cell layer3.29e-11309
endo-epithelium3.45e-1182
epithelium3.53e-11306
urinary system structure3.67e-1147
multi-cellular organism5.47e-11656
renal system7.79e-1148
trunk region element1.50e-10101
subdivision of trunk3.86e-10112
anatomical system3.00e-09624
trunk mesenchyme4.52e-09122
epithelial tube4.72e-09117
anatomical group5.18e-09625
subdivision of digestive tract5.28e-09118
primordium5.29e-09160
gut epithelium9.32e-0954
abdomen element2.51e-0854
abdominal segment element2.51e-0854
head5.33e-0856
abdominal segment of trunk5.65e-0860
abdomen5.65e-0860
subdivision of head8.65e-0849
ectodermal placode1.32e-0731
immaterial anatomical entity1.78e-07117
respiratory system2.05e-0774
foregut2.56e-0787
gland2.71e-0759
exocrine gland5.26e-0731
exocrine system5.26e-0731
anterior region of body8.37e-0762
craniocervical region8.37e-0762
Disease
Ontology termp-valuen
cell type cancer3.11e-12143
carcinoma4.60e-12106
disease of anatomical entity5.11e-0939


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#90556.336201576962639.78880505817628e-050.00138979474098814
CHD2#1106510.34402283411698.43981772346334e-060.000230142590919266
CTBP2#1488562.71700033932811.02712351233917e-099.50148383571214e-08
CTCF#1066455.360256373075030.0002259278299937090.00249663280464638
E2F1#186954.907389214879320.0003512818099256460.00352493475661266
E2F6#187655.017155731697390.0003144978599297790.00322650707202418
EGR1#195854.988179094810140.0003237398000590710.00330638186762853
ELF1#199754.258097958807540.0007142416939776840.00572835879875099
HDAC2#3066410.7324961893010.0001450965797478750.00188549728658558
IRF1#365957.63716375356393.84754333311872e-050.000723763649437295
JUND#372756.994663941871035.97069468343598e-050.000983709389562028
MXI1#460159.96157162875931.01894348670516e-050.000266509989501628
MYC#460955.22228187160940.0002573944848850610.00276336581074331
RFX5#5993512.04791082719513.93714721313598e-060.000127461784808651
SMARCB1#6598518.25271578115744.93125075403021e-072.31467369662994e-05
SP1#666755.69838137814090.000166391843712550.00204156458711173
SRF#6722513.79717826216781.9987012616697e-067.31915712017959e-05
TAF1#687253.343046285745290.002394600090870310.0135264015842071
TBP#690853.706770687096390.001428755106721120.00918263105174445
TCF7L2#6934510.77017656313736.89693748574565e-060.000199697603014635
TRIM28#10155518.59052504526254.49912775886781e-072.13583820003816e-05
ZBTB7A#5134157.35190930787594.65425347594289e-050.000815443010860592
ZNF263#1012758.221841637010682.6606316672286e-050.000570816989921299



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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