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Coexpression cluster:C950: Difference between revisions

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|full_id=C950_liposarcoma_extraskeletal_Fibroblast_Smooth_Preadipocyte_neuroblastoma_mesenchymal
|full_id=C950_liposarcoma_extraskeletal_Fibroblast_Smooth_Preadipocyte_neuroblastoma_mesenchymal
|id=C950
|id=C950
|ontology_enrichment_celltype=CL:0000055!4.66e-27!180;CL:0000183!4.48e-18!59;CL:0000680!4.51e-18!57;CL:0000056!4.51e-18!57;CL:0000355!4.51e-18!57;CL:0000187!2.14e-16!54;CL:0000057!4.71e-16!75;CL:0000393!1.76e-14!60;CL:0000211!1.76e-14!60;CL:0000192!1.33e-12!42;CL:0000514!1.33e-12!42;CL:0000359!3.68e-10!32;CL:0000222!1.58e-08!119;CL:0002620!2.63e-08!23
|ontology_enrichment_celltype=CL:0000183!7.68e-23!59;CL:0000680!2.11e-22!58;CL:0000056!2.11e-22!58;CL:0000355!2.11e-22!58;CL:0000187!3.97e-20!55;CL:0000057!4.74e-20!76;CL:0000393!1.71e-17!61;CL:0000211!1.71e-17!61;CL:0000192!2.43e-16!43;CL:0000514!2.43e-16!43;CL:0002620!4.24e-14!23;CL:0000359!5.08e-14!32;CL:0000055!1.43e-10!106;CL:0002539!9.64e-10!10;CL:0000048!2.70e-08!427;CL:0000723!1.06e-07!433;CL:0000034!5.95e-07!441;CL:0000222!5.95e-07!121
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:2394!1.55e-08!14
|ontology_enrichment_uberon=UBERON:0000475!8.98e-27!365;UBERON:0004290!3.26e-23!70;UBERON:0000914!3.02e-22!83;UBERON:0002329!3.02e-22!83;UBERON:0003077!3.02e-22!83;UBERON:0003059!3.02e-22!83;UBERON:0007282!3.02e-22!83;UBERON:0009618!3.02e-22!83;UBERON:0007285!3.02e-22!83;UBERON:0000119!1.10e-21!312;UBERON:0000483!2.81e-20!309;UBERON:0002385!1.94e-19!63;UBERON:0001015!1.94e-19!63;UBERON:0000383!1.94e-19!63;UBERON:0001134!2.63e-19!61;UBERON:0002036!2.63e-19!61;UBERON:0003082!2.63e-19!61;UBERON:0000481!2.14e-18!347;UBERON:0000073!2.89e-17!94;UBERON:0001016!2.89e-17!94;UBERON:0000486!4.04e-17!82;UBERON:0005743!9.43e-17!86;UBERON:0001017!1.86e-16!82;UBERON:0003075!2.20e-16!86;UBERON:0007284!2.20e-16!86;UBERON:0002346!5.64e-16!90;UBERON:0000955!1.05e-15!69;UBERON:0006238!1.05e-15!69;UBERON:0002616!2.07e-15!59;UBERON:0000153!7.45e-15!129;UBERON:0007811!7.45e-15!129;UBERON:0000033!1.61e-14!123;UBERON:0000468!1.75e-14!659;UBERON:0007023!2.02e-14!115;UBERON:0004121!3.11e-14!169;UBERON:0000924!3.91e-14!173;UBERON:0006601!3.91e-14!173;UBERON:0001049!1.04e-13!57;UBERON:0005068!1.04e-13!57;UBERON:0006241!1.04e-13!57;UBERON:0007135!1.04e-13!57;UBERON:0000025!1.68e-13!194;UBERON:0000477!1.84e-13!286;UBERON:0003056!2.40e-13!61;UBERON:0005256!1.61e-12!143;UBERON:0000467!6.84e-12!625;UBERON:0003080!8.68e-12!42;UBERON:0002780!8.83e-12!41;UBERON:0001890!8.83e-12!41;UBERON:0006240!8.83e-12!41;UBERON:0000480!1.10e-11!626;UBERON:0001893!4.27e-11!34;UBERON:0004111!5.68e-11!241;UBERON:0001869!7.89e-11!32;UBERON:0002791!1.02e-10!33;UBERON:0002049!1.21e-10!79;UBERON:0007798!1.21e-10!79;UBERON:0002020!1.46e-10!34;UBERON:0003528!1.46e-10!34;UBERON:0002619!3.01e-10!22;UBERON:0004872!3.26e-10!84;UBERON:0000479!3.74e-10!787;UBERON:0000956!5.63e-10!25;UBERON:0000203!5.63e-10!25;UBERON:0001950!9.78e-10!20;UBERON:0000922!1.33e-09!612;UBERON:0002050!1.46e-09!605;UBERON:0005423!1.46e-09!605;UBERON:0000923!2.69e-09!604;UBERON:0005291!2.69e-09!604;UBERON:0006598!2.69e-09!604;UBERON:0002532!2.69e-09!604;UBERON:0001637!7.28e-09!42;UBERON:0003509!7.28e-09!42;UBERON:0004572!7.28e-09!42;UBERON:0004573!1.45e-08!33;UBERON:0004571!1.45e-08!33;UBERON:0001009!1.70e-08!113;UBERON:0004535!2.56e-08!110;UBERON:0001981!8.80e-08!60;UBERON:0007500!8.80e-08!60;UBERON:0004537!8.80e-08!60;UBERON:0006965!8.80e-08!60;UBERON:0002100!2.32e-07!216;UBERON:0002199!2.44e-07!45;UBERON:0002416!2.44e-07!45;UBERON:0001135!2.85e-07!15;UBERON:0001013!5.74e-07!14;UBERON:0000948!8.09e-07!24;UBERON:0005498!8.09e-07!24;UBERON:0004140!8.09e-07!24;UBERON:0009881!8.09e-07!24;UBERON:0004141!8.09e-07!24;UBERON:0003084!8.09e-07!24;UBERON:0007005!8.09e-07!24;UBERON:0004139!8.09e-07!24;UBERON:0004291!8.09e-07!24;UBERON:0007100!8.28e-07!27;UBERON:0000055!8.42e-07!69;UBERON:0000064!8.43e-07!219
|ontology_enrichment_uberon=UBERON:0002329!7.03e-25!71;UBERON:0003059!7.03e-25!71;UBERON:0007282!7.03e-25!71;UBERON:0004290!7.03e-25!71;UBERON:0009618!7.03e-25!71;UBERON:0003077!2.97e-24!72;UBERON:0007285!2.97e-24!72;UBERON:0007503!7.99e-24!78;UBERON:0007524!1.20e-23!73;UBERON:0001134!2.10e-22!62;UBERON:0002036!2.10e-22!62;UBERON:0003082!2.10e-22!62;UBERON:0002385!5.11e-22!64;UBERON:0001015!5.11e-22!64;UBERON:0000383!5.11e-22!64;UBERON:0000486!1.35e-19!83;UBERON:0005256!8.86e-15!122;UBERON:0002049!1.17e-13!78;UBERON:0007798!1.17e-13!78;UBERON:0001637!1.31e-12!42;UBERON:0003509!1.31e-12!42;UBERON:0004572!1.31e-12!42;UBERON:0004573!3.00e-12!33;UBERON:0004571!3.00e-12!33;UBERON:0000119!4.54e-12!309;UBERON:0004535!1.68e-11!109;UBERON:0000483!8.38e-11!306;UBERON:0001009!9.66e-11!112;UBERON:0004872!1.25e-10!83;UBERON:0000947!2.25e-10!21;UBERON:0010191!2.25e-10!21;UBERON:0001135!3.18e-10!15;UBERON:0000479!3.63e-10!773;UBERON:0000490!3.73e-10!148;UBERON:0003104!6.69e-10!160;UBERON:0009142!6.69e-10!160;UBERON:0004237!9.64e-10!10;UBERON:0004695!9.64e-10!10;UBERON:0002111!9.64e-10!10;UBERON:0004178!9.64e-10!10;UBERON:0007500!1.67e-09!59;UBERON:0001981!1.67e-09!59;UBERON:0004537!1.67e-09!59;UBERON:0006965!1.67e-09!59;UBERON:0000468!1.67e-08!656;UBERON:0000055!2.19e-08!68;UBERON:0000481!2.24e-08!342;UBERON:0002199!2.92e-08!46;UBERON:0002416!2.92e-08!46;UBERON:0006876!3.25e-08!11;UBERON:0000467!4.85e-08!624;UBERON:0000480!6.01e-08!625;UBERON:0000475!6.75e-08!264;UBERON:0003914!1.14e-07!117;UBERON:0000926!4.47e-07!315;UBERON:0004120!4.47e-07!315;UBERON:0006603!4.47e-07!315;UBERON:0002100!5.12e-07!199;UBERON:0010314!6.46e-07!132
|tf_chipseq_enrich=EP300#2033;9:6.7739417262232:3.3261238408136e-08:2.22963445321394e-06!GATA2#2624;8:11.3288282076035:1.20057232306882e-08:8.94979106702244e-07!RAD21#5885;9:10.3550338954563:7.29196863888313e-10:6.91703826227353e-08!YY1#7528;9:4.91117074985386:6.01179022795762e-07:2.76227610918463e-05
|tf_chipseq_enrich=EP300#2033;9:6.7739417262232:3.3261238408136e-08:2.22963445321394e-06!GATA2#2624;8:11.3288282076035:1.20057232306882e-08:8.94979106702244e-07!RAD21#5885;9:10.3550338954563:7.29196863888313e-10:6.91703826227353e-08!YY1#7528;9:4.91117074985386:6.01179022795762e-07:2.76227610918463e-05
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}}
}}

Revision as of 16:54, 19 October 2012


Full id: C950_liposarcoma_extraskeletal_Fibroblast_Smooth_Preadipocyte_neuroblastoma_mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:14440817..14440832,+p24@TRIO
Hg19::chr5:14440848..14440864,+p22@TRIO
Hg19::chr5:14440872..14440890,+p13@TRIO
Hg19::chr5:14440903..14440920,+p6@TRIO
Hg19::chr5:14440934..14440949,+p10@TRIO
Hg19::chr5:14441117..14441141,+p5@TRIO
Hg19::chr5:14441157..14441216,+p3@TRIO
Hg19::chr5:14441222..14441241,+p4@TRIO
Hg19::chr5:14441335..14441346,+p18@TRIO


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
somite7.03e-2571
presomitic mesoderm7.03e-2571
presumptive segmental plate7.03e-2571
dermomyotome7.03e-2571
trunk paraxial mesoderm7.03e-2571
paraxial mesoderm2.97e-2472
presumptive paraxial mesoderm2.97e-2472
epithelial vesicle7.99e-2478
dense mesenchyme tissue1.20e-2373
skeletal muscle tissue2.10e-2262
striated muscle tissue2.10e-2262
myotome2.10e-2262
muscle tissue5.11e-2264
musculature5.11e-2264
musculature of body5.11e-2264
multilaminar epithelium1.35e-1983
trunk mesenchyme8.86e-15122
vasculature1.17e-1378
vascular system1.17e-1378
artery1.31e-1242
arterial blood vessel1.31e-1242
arterial system1.31e-1242
systemic artery3.00e-1233
systemic arterial system3.00e-1233
cell layer4.54e-12309
cardiovascular system1.68e-11109
epithelium8.38e-11306
circulatory system9.66e-11112
splanchnic layer of lateral plate mesoderm1.25e-1083
aorta2.25e-1021
aortic system2.25e-1021
smooth muscle tissue3.18e-1015
tissue3.63e-10773
unilaminar epithelium3.73e-10148
mesenchyme6.69e-10160
entire embryonic mesenchyme6.69e-10160
blood vessel smooth muscle9.64e-1010
arterial system smooth muscle9.64e-1010
artery smooth muscle tissue9.64e-1010
aorta smooth muscle tissue9.64e-1010
epithelial tube open at both ends1.67e-0959
blood vessel1.67e-0959
blood vasculature1.67e-0959
vascular cord1.67e-0959
multi-cellular organism1.67e-08656
vessel2.19e-0868
multi-tissue structure2.24e-08342
integument2.92e-0846
integumental system2.92e-0846
vasculature of organ3.25e-0811
anatomical system4.85e-08624
anatomical group6.01e-08625
organism subdivision6.75e-08264
epithelial tube1.14e-07117
mesoderm4.47e-07315
mesoderm-derived structure4.47e-07315
presumptive mesoderm4.47e-07315
trunk5.12e-07199
structure with developmental contribution from neural crest6.46e-07132
Disease
Ontology termp-valuen
ovarian cancer1.55e-0814


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
EP300#203396.77394172622323.3261238408136e-082.22963445321394e-06
GATA2#2624811.32882820760351.20057232306882e-088.94979106702244e-07
RAD21#5885910.35503389545637.29196863888313e-106.91703826227353e-08
YY1#752894.911170749853866.01179022795762e-072.76227610918463e-05



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C950&oldid=2251772"