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Coexpression cluster:C2093: Difference between revisions

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|full_id=C2093_mesenchymal_mucinous_bile_Fibroblast_lung_Smooth_liposarcoma
|full_id=C2093_mesenchymal_mucinous_bile_Fibroblast_lung_Smooth_liposarcoma
|id=C2093
|id=C2093
|ontology_enrichment_celltype=CL:0000548!1.64e-27!679;CL:0000004!1.64e-27!679;CL:0000255!1.64e-27!679;CL:0000012!8.84e-27!682;CL:0000055!1.73e-25!180;CL:0002371!3.13e-24!591;CL:0000144!7.13e-24!625;CL:0000220!4.73e-21!246;CL:0002321!2.01e-20!248;CL:0000003!1.70e-18!722;CL:0000222!5.98e-18!119;CL:0000680!2.47e-14!57;CL:0000056!2.47e-14!57;CL:0000355!2.47e-14!57;CL:0000187!4.19e-13!54;CL:0000183!7.66e-13!59;CL:0000057!2.15e-12!75;CL:0000393!3.86e-12!60;CL:0000211!3.86e-12!60;CL:0000192!1.78e-11!42;CL:0000514!1.78e-11!42;CL:0002620!1.46e-10!23;CL:0000359!2.35e-10!32;CL:0000723!1.23e-08!436;CL:0000048!2.78e-08!430;CL:0000034!1.08e-07!444;CL:0000063!1.44e-07!578;CL:0002139!6.55e-07!24
|ontology_enrichment_celltype=CL:0000548!7.84e-20!679;CL:0000255!7.84e-20!679;CL:0002371!5.12e-18!588;CL:0002321!3.17e-14!250;CL:0000003!1.10e-13!722;CL:0000222!1.55e-12!121;CL:0000680!5.90e-11!58;CL:0000056!5.90e-11!58;CL:0000355!5.90e-11!58;CL:0000057!6.87e-11!76;CL:0002620!1.90e-10!23;CL:0000187!1.19e-09!55;CL:0000183!1.72e-09!59;CL:0000055!2.12e-09!106;CL:0000192!1.50e-08!43;CL:0000514!1.50e-08!43;CL:0000393!3.73e-08!61;CL:0000211!3.73e-08!61;CL:0000359!6.54e-08!32
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!6.86e-16!79;UBERON:0007798!6.86e-16!79;UBERON:0000914!5.77e-15!83;UBERON:0002329!5.77e-15!83;UBERON:0003077!5.77e-15!83;UBERON:0003059!5.77e-15!83;UBERON:0007282!5.77e-15!83;UBERON:0009618!5.77e-15!83;UBERON:0007285!5.77e-15!83;UBERON:0004290!1.00e-13!70;UBERON:0000490!4.76e-13!138;UBERON:0001637!6.36e-13!42;UBERON:0003509!6.36e-13!42;UBERON:0004572!6.36e-13!42;UBERON:0004573!1.06e-12!33;UBERON:0004571!1.06e-12!33;UBERON:0005256!1.13e-12!143;UBERON:0001134!4.17e-12!61;UBERON:0002036!4.17e-12!61;UBERON:0003082!4.17e-12!61;UBERON:0001981!5.70e-12!60;UBERON:0007500!5.70e-12!60;UBERON:0004537!5.70e-12!60;UBERON:0006965!5.70e-12!60;UBERON:0000055!6.90e-12!69;UBERON:0000486!8.79e-12!82;UBERON:0002385!3.98e-11!63;UBERON:0001015!3.98e-11!63;UBERON:0000383!3.98e-11!63;UBERON:0004535!8.24e-11!110;UBERON:0004872!2.62e-10!84;UBERON:0003914!3.55e-10!118;UBERON:0001009!7.16e-10!113;UBERON:0002204!1.95e-09!167;UBERON:0000467!2.70e-09!625;UBERON:0000480!3.83e-09!626;UBERON:0002100!5.67e-08!216;UBERON:0000468!7.02e-08!659;UBERON:0003102!1.03e-07!95;UBERON:0000947!5.40e-07!21;UBERON:0010191!5.40e-07!21;UBERON:0000926!5.69e-07!448;UBERON:0004120!5.69e-07!448;UBERON:0006603!5.69e-07!448;UBERON:0000475!8.03e-07!365
|ontology_enrichment_uberon=UBERON:0002049!7.14e-12!78;UBERON:0007798!7.14e-12!78;UBERON:0000490!1.56e-11!148;UBERON:0004573!4.94e-11!33;UBERON:0004571!4.94e-11!33;UBERON:0001637!1.02e-10!42;UBERON:0003509!1.02e-10!42;UBERON:0004572!1.02e-10!42;UBERON:0002204!1.37e-09!167;UBERON:0001134!1.94e-09!62;UBERON:0002036!1.94e-09!62;UBERON:0003082!1.94e-09!62;UBERON:0002329!5.47e-09!71;UBERON:0003059!5.47e-09!71;UBERON:0007282!5.47e-09!71;UBERON:0004290!5.47e-09!71;UBERON:0009618!5.47e-09!71;UBERON:0007503!7.90e-09!78;UBERON:0002385!9.10e-09!64;UBERON:0001015!9.10e-09!64;UBERON:0000383!9.10e-09!64;UBERON:0003077!1.10e-08!72;UBERON:0007285!1.10e-08!72;UBERON:0000467!1.12e-08!624;UBERON:0000480!1.43e-08!625;UBERON:0007500!1.69e-08!59;UBERON:0001981!1.69e-08!59;UBERON:0004537!1.69e-08!59;UBERON:0006965!1.69e-08!59;UBERON:0007524!2.15e-08!73;UBERON:0000055!4.50e-08!68;UBERON:0004535!6.06e-08!109;UBERON:0001009!2.51e-07!112;UBERON:0003914!3.00e-07!117;UBERON:0005256!7.08e-07!122;UBERON:0000486!8.45e-07!83
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00267485009124437!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00433500345534657!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00194558326379309!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000303087760453759!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000719815699074957!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000741806725714111!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00390987918120953!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000441905924805984!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129062143639157!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00122873148497025!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482683326449362
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00267485009124437!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00433500345534657!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00194558326379309!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000303087760453759!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000719815699074957!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000741806725714111!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00390987918120953!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000441905924805984!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129062143639157!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00122873148497025!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482683326449362
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}}
}}

Revision as of 12:03, 19 October 2012


Full id: C2093_mesenchymal_mucinous_bile_Fibroblast_lung_Smooth_liposarcoma



Phase1 CAGE Peaks

Hg19::chr11:108800197..108800208,+p6@DDX10
Hg19::chr11:108800225..108800254,+p4@DDX10
Hg19::chr11:108800264..108800294,+p3@DDX10
Hg19::chr11:108800302..108800338,+p2@DDX10


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
vasculature7.14e-1278
vascular system7.14e-1278
unilaminar epithelium1.56e-11148
systemic artery4.94e-1133
systemic arterial system4.94e-1133
artery1.02e-1042
arterial blood vessel1.02e-1042
arterial system1.02e-1042
musculoskeletal system1.37e-09167
skeletal muscle tissue1.94e-0962
striated muscle tissue1.94e-0962
myotome1.94e-0962
somite5.47e-0971
presomitic mesoderm5.47e-0971
presumptive segmental plate5.47e-0971
dermomyotome5.47e-0971
trunk paraxial mesoderm5.47e-0971
epithelial vesicle7.90e-0978
muscle tissue9.10e-0964
musculature9.10e-0964
musculature of body9.10e-0964
paraxial mesoderm1.10e-0872
presumptive paraxial mesoderm1.10e-0872
anatomical system1.12e-08624
anatomical group1.43e-08625
epithelial tube open at both ends1.69e-0859
blood vessel1.69e-0859
blood vasculature1.69e-0859
vascular cord1.69e-0859
dense mesenchyme tissue2.15e-0873
vessel4.50e-0868
cardiovascular system6.06e-08109
circulatory system2.51e-07112
epithelial tube3.00e-07117
trunk mesenchyme7.08e-07122
multilaminar epithelium8.45e-0783


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#105147.971147625824820.0002476385788090830.00267485009124437
EP300#203346.77394172622320.0004748459821442640.00433500345534657
FOS#235348.99795530889440.0001525147711168630.00194558326379309
FOSL2#2355416.93020060456171.2165416097647e-050.000303087760453759
GATA2#2624412.7449317335543.78864877853583e-050.000719815699074957
JUN#3725412.51282919233634.07770316866756e-050.000741806725714111
JUND#372746.994663941871030.000417684217818580.00390987918120953
NR3C1#2908414.9730233311731.98868032687801e-050.000441905924805984
RAD21#5885410.35503389545638.6948481184721e-050.00129062143639157
STAT3#6774410.51946499715428.16377768286615e-050.00122873148497025
USF1#739134.771124457905970.01370465887188020.0482683326449362



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.