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Coexpression cluster:C2907: Difference between revisions

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|full_id=C2907_mesenchymal_myxofibrosarcoma_serous_Smooth_Endothelial_leiomyoma_Fibroblast
|full_id=C2907_mesenchymal_myxofibrosarcoma_serous_Smooth_Endothelial_leiomyoma_Fibroblast
|id=C2907
|id=C2907
|ontology_enrichment_celltype=CL:0000055!1.81e-29!180;CL:0000222!5.79e-25!119;CL:0000183!9.61e-21!59;CL:0000680!1.52e-20!57;CL:0000056!1.52e-20!57;CL:0000355!1.52e-20!57;CL:0000187!1.55e-19!54;CL:0000192!1.27e-18!42;CL:0000514!1.27e-18!42;CL:0000393!6.65e-18!60;CL:0000211!6.65e-18!60;CL:0000359!1.78e-16!32;CL:0002139!5.73e-14!24;CL:0000057!1.97e-12!75;CL:0000115!2.38e-12!35;CL:0000071!3.73e-11!18;CL:0002546!3.73e-11!18;CL:0002078!2.05e-10!44;CL:0000220!2.19e-09!246;CL:0002321!6.21e-09!248;CL:0000213!2.23e-07!57;CL:0000215!2.23e-07!57
|ontology_enrichment_celltype=CL:0000222!1.85e-25!121;CL:0000680!3.59e-20!58;CL:0000056!3.59e-20!58;CL:0000355!3.59e-20!58;CL:0000183!7.30e-20!59;CL:0000187!4.00e-19!55;CL:0000192!1.83e-18!43;CL:0000514!1.83e-18!43;CL:0000393!8.41e-18!61;CL:0000211!8.41e-18!61;CL:0000359!1.03e-16!32;CL:0000055!4.53e-16!106;CL:0002139!3.92e-14!24;CL:0000115!2.41e-13!36;CL:0000057!9.05e-13!76;CL:0002078!1.83e-11!45;CL:0000071!2.53e-11!18;CL:0002546!2.53e-11!18;CL:0002321!5.73e-08!250;CL:0000213!6.69e-08!58;CL:0000215!6.69e-08!58
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004535!4.73e-36!110;UBERON:0001009!1.64e-35!113;UBERON:0002049!4.85e-34!79;UBERON:0007798!4.85e-34!79;UBERON:0000055!2.06e-28!69;UBERON:0004872!1.06e-26!84;UBERON:0001981!3.79e-26!60;UBERON:0007500!3.79e-26!60;UBERON:0004537!3.79e-26!60;UBERON:0006965!3.79e-26!60;UBERON:0000477!1.37e-25!286;UBERON:0000914!1.84e-22!83;UBERON:0002329!1.84e-22!83;UBERON:0003077!1.84e-22!83;UBERON:0003059!1.84e-22!83;UBERON:0007282!1.84e-22!83;UBERON:0009618!1.84e-22!83;UBERON:0007285!1.84e-22!83;UBERON:0004290!3.01e-22!70;UBERON:0003914!3.17e-22!118;UBERON:0000119!2.61e-21!312;UBERON:0001637!8.73e-21!42;UBERON:0003509!8.73e-21!42;UBERON:0004572!8.73e-21!42;UBERON:0000483!5.70e-20!309;UBERON:0001134!1.33e-19!61;UBERON:0002036!1.33e-19!61;UBERON:0003082!1.33e-19!61;UBERON:0002385!2.12e-19!63;UBERON:0001015!2.12e-19!63;UBERON:0000383!2.12e-19!63;UBERON:0004111!1.92e-18!241;UBERON:0000025!1.70e-17!194;UBERON:0000490!3.23e-17!138;UBERON:0005256!3.70e-17!143;UBERON:0000475!5.02e-17!365;UBERON:0000486!1.73e-16!82;UBERON:0004573!3.20e-16!33;UBERON:0004571!3.20e-16!33;UBERON:0000481!4.99e-16!347;UBERON:0000468!9.02e-16!659;UBERON:0000467!7.02e-15!625;UBERON:0000480!1.40e-14!626;UBERON:0002100!2.74e-12!216;UBERON:0001986!3.73e-11!18;UBERON:0004638!3.73e-11!18;UBERON:0004852!3.73e-11!18;UBERON:0000487!4.48e-11!22;UBERON:0002050!2.77e-10!605;UBERON:0005423!2.77e-10!605;UBERON:0000923!2.96e-10!604;UBERON:0005291!2.96e-10!604;UBERON:0006598!2.96e-10!604;UBERON:0002532!2.96e-10!604;UBERON:0006914!4.51e-10!25;UBERON:0000922!5.05e-10!612;UBERON:0003104!5.24e-10!238;UBERON:0009142!5.24e-10!238;UBERON:0000947!1.45e-09!21;UBERON:0010191!1.45e-09!21;UBERON:0000948!3.81e-07!24;UBERON:0005498!3.81e-07!24;UBERON:0004140!3.81e-07!24;UBERON:0009881!3.81e-07!24;UBERON:0004141!3.81e-07!24;UBERON:0003084!3.81e-07!24;UBERON:0007005!3.81e-07!24;UBERON:0004139!3.81e-07!24;UBERON:0004291!3.81e-07!24;UBERON:0007100!9.92e-07!27
|ontology_enrichment_uberon=UBERON:0004535!2.42e-35!109;UBERON:0001009!1.24e-34!112;UBERON:0002049!1.59e-33!78;UBERON:0007798!1.59e-33!78;UBERON:0000055!5.89e-28!68;UBERON:0007500!7.34e-26!59;UBERON:0001981!7.34e-26!59;UBERON:0004537!7.34e-26!59;UBERON:0006965!7.34e-26!59;UBERON:0004872!7.49e-26!83;UBERON:0007503!2.68e-23!78;UBERON:0003914!1.16e-22!117;UBERON:0003077!6.03e-22!72;UBERON:0007285!6.03e-22!72;UBERON:0002329!6.67e-22!71;UBERON:0003059!6.67e-22!71;UBERON:0007282!6.67e-22!71;UBERON:0004290!6.67e-22!71;UBERON:0009618!6.67e-22!71;UBERON:0007524!6.73e-22!73;UBERON:0000119!8.84e-21!309;UBERON:0001637!9.67e-21!42;UBERON:0003509!9.67e-21!42;UBERON:0004572!9.67e-21!42;UBERON:0000477!1.11e-20!373;UBERON:0000490!1.44e-19!148;UBERON:0000483!1.99e-19!306;UBERON:0001134!2.04e-19!62;UBERON:0002036!2.04e-19!62;UBERON:0003082!2.04e-19!62;UBERON:0002385!2.62e-19!64;UBERON:0001015!2.62e-19!64;UBERON:0000383!2.62e-19!64;UBERON:0004111!7.76e-18!240;UBERON:0000025!8.22e-18!192;UBERON:0004573!2.43e-16!33;UBERON:0004571!2.43e-16!33;UBERON:0000486!5.23e-16!83;UBERON:0005256!1.17e-15!122;UBERON:0003104!2.88e-15!160;UBERON:0009142!2.88e-15!160;UBERON:0000481!6.10e-15!342;UBERON:0000468!4.32e-14!656;UBERON:0000467!6.91e-14!624;UBERON:0000480!1.25e-13!625;UBERON:0000487!2.11e-11!22;UBERON:0004638!2.53e-11!18;UBERON:0001986!2.53e-11!18;UBERON:0004852!2.53e-11!18;UBERON:0002100!4.04e-11!199;UBERON:0000475!1.36e-10!264;UBERON:0006914!1.94e-10!25;UBERON:0010314!5.07e-10!132;UBERON:0000947!1.68e-09!21;UBERON:0010191!1.68e-09!21;UBERON:0000926!1.95e-09!315;UBERON:0004120!1.95e-09!315;UBERON:0006603!1.95e-09!315;UBERON:0000922!1.54e-08!592;UBERON:0005423!6.30e-08!581;UBERON:0000923!7.14e-08!560;UBERON:0010316!7.14e-08!560;UBERON:0005291!7.14e-08!560;UBERON:0006598!7.14e-08!560;UBERON:0010317!7.14e-08!560;UBERON:0002532!7.14e-08!560;UBERON:0002050!1.88e-07!564;UBERON:0000948!8.14e-07!24;UBERON:0005498!8.14e-07!24;UBERON:0004140!8.14e-07!24;UBERON:0009881!8.14e-07!24;UBERON:0004141!8.14e-07!24;UBERON:0003084!8.14e-07!24;UBERON:0007005!8.14e-07!24;UBERON:0004139!8.14e-07!24;UBERON:0004291!8.14e-07!24
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820090848764771!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00200183033956962!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195513565492501!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000724826323102224!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000444744720896814!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172786911384544!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157570938782144!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000242306927885548!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000327493061112711!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114920506637219
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}}
}}

Revision as of 14:33, 19 October 2012


Full id: C2907_mesenchymal_myxofibrosarcoma_serous_Smooth_Endothelial_leiomyoma_Fibroblast



Phase1 CAGE Peaks

Hg19::chr7:93551154..93551186,+p4@GNG11
Hg19::chr7:93551194..93551205,+p9@GNG11
Hg19::chr7:93551224..93551235,+p8@GNG11
Hg19::chr7:93551243..93551254,+p10@GNG11


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
cardiovascular system2.42e-35109
circulatory system1.24e-34112
vasculature1.59e-3378
vascular system1.59e-3378
vessel5.89e-2868
epithelial tube open at both ends7.34e-2659
blood vessel7.34e-2659
blood vasculature7.34e-2659
vascular cord7.34e-2659
splanchnic layer of lateral plate mesoderm7.49e-2683
epithelial vesicle2.68e-2378
epithelial tube1.16e-22117
paraxial mesoderm6.03e-2272
presumptive paraxial mesoderm6.03e-2272
somite6.67e-2271
presomitic mesoderm6.67e-2271
presumptive segmental plate6.67e-2271
dermomyotome6.67e-2271
trunk paraxial mesoderm6.67e-2271
dense mesenchyme tissue6.73e-2273
cell layer8.84e-21309
artery9.67e-2142
arterial blood vessel9.67e-2142
arterial system9.67e-2142
anatomical cluster1.11e-20373
unilaminar epithelium1.44e-19148
epithelium1.99e-19306
skeletal muscle tissue2.04e-1962
striated muscle tissue2.04e-1962
myotome2.04e-1962
muscle tissue2.62e-1964
musculature2.62e-1964
musculature of body2.62e-1964
anatomical conduit7.76e-18240
tube8.22e-18192
systemic artery2.43e-1633
systemic arterial system2.43e-1633
multilaminar epithelium5.23e-1683
trunk mesenchyme1.17e-15122
mesenchyme2.88e-15160
entire embryonic mesenchyme2.88e-15160
multi-tissue structure6.10e-15342
multi-cellular organism4.32e-14656
anatomical system6.91e-14624
anatomical group1.25e-13625
simple squamous epithelium2.11e-1122
blood vessel endothelium2.53e-1118
endothelium2.53e-1118
cardiovascular system endothelium2.53e-1118
trunk4.04e-11199
organism subdivision1.36e-10264
squamous epithelium1.94e-1025
structure with developmental contribution from neural crest5.07e-10132
aorta1.68e-0921
aortic system1.68e-0921
mesoderm1.95e-09315
mesoderm-derived structure1.95e-09315
presumptive mesoderm1.95e-09315
embryo1.54e-08592
developing anatomical structure6.30e-08581
germ layer7.14e-08560
germ layer / neural crest7.14e-08560
embryonic tissue7.14e-08560
presumptive structure7.14e-08560
germ layer / neural crest derived structure7.14e-08560
epiblast (generic)7.14e-08560
embryonic structure1.88e-07564
heart8.14e-0724
primitive heart tube8.14e-0724
primary heart field8.14e-0724
anterior lateral plate mesoderm8.14e-0724
heart tube8.14e-0724
heart primordium8.14e-0724
cardiac mesoderm8.14e-0724
cardiogenic plate8.14e-0724
heart rudiment8.14e-0724


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
CTCF#1066445.360256373075030.001211145381643620.00820090848764771
EBF1#187948.9064668465690.00015887907472010.00200183033956962
FOS#235348.99795530889440.0001525147711168630.00195513565492501
GATA2#2624412.7449317335543.78864877853583e-050.000724826323102224
NR3C1#2908414.9730233311731.98868032687801e-050.000444744720896814
RAD21#588537.766275421592250.0033411193858720.0172786911384544
REST#597849.650028716128020.0001152825614219170.00157570938782144
SMARCB1#6598418.25271578115749.00423392720929e-060.000242306927885548
TFAP2A#7020416.5186343730451.34240829060362e-050.000327493061112711
TFAP2C#7022410.80922860986027.32289634782688e-050.00114920506637219



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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