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Coexpression cluster:C2716: Difference between revisions

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|full_id=C2716_Osteoblast_leiomyoma_Preadipocyte_Adipocyte_mesenchymal_Smooth_Mesothelial
|full_id=C2716_Osteoblast_leiomyoma_Preadipocyte_Adipocyte_mesenchymal_Smooth_Mesothelial
|id=C2716
|id=C2716
|ontology_enrichment_celltype=CL:0000055!1.08e-31!180;CL:0000057!2.49e-16!75;CL:0000222!1.10e-14!119;CL:0000680!6.74e-13!57;CL:0000056!6.74e-13!57;CL:0000355!6.74e-13!57;CL:0000220!6.93e-13!246;CL:0002321!8.24e-13!248;CL:0000183!1.72e-12!59;CL:0000192!4.11e-12!42;CL:0000514!4.11e-12!42;CL:0000187!1.47e-11!54;CL:0000359!1.54e-10!32;CL:0000393!4.41e-10!60;CL:0000211!4.41e-10!60;CL:0000136!8.89e-10!15;CL:0000548!1.15e-07!679;CL:0000004!1.15e-07!679;CL:0000255!1.15e-07!679;CL:0002334!1.79e-07!12;CL:0000012!4.00e-07!682
|ontology_enrichment_celltype=CL:0000057!9.61e-17!76;CL:0000222!7.63e-15!121;CL:0000055!5.02e-14!106;CL:0002321!8.18e-13!250;CL:0000680!1.54e-12!58;CL:0000056!1.54e-12!58;CL:0000355!1.54e-12!58;CL:0000183!8.75e-12!59;CL:0000192!9.56e-12!43;CL:0000514!9.56e-12!43;CL:0000187!2.99e-11!55;CL:0000359!1.95e-10!32;CL:0000393!1.01e-09!61;CL:0000211!1.01e-09!61;CL:0000136!1.13e-09!15;CL:0000548!7.62e-08!679;CL:0000255!7.62e-08!679;CL:0002334!2.30e-07!12;CL:0000349!4.18e-07!19
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!2.16e-19!118;UBERON:0002100!1.96e-18!216;UBERON:0005256!5.05e-18!143;UBERON:0000468!2.27e-17!659;UBERON:0004872!8.25e-17!84;UBERON:0000475!2.78e-14!365;UBERON:0000467!4.86e-14!625;UBERON:0000480!7.79e-14!626;UBERON:0000486!1.53e-13!82;UBERON:0003104!2.68e-13!238;UBERON:0009142!2.68e-13!238;UBERON:0000914!2.86e-13!83;UBERON:0002329!2.86e-13!83;UBERON:0003077!2.86e-13!83;UBERON:0003059!2.86e-13!83;UBERON:0007282!2.86e-13!83;UBERON:0009618!2.86e-13!83;UBERON:0007285!2.86e-13!83;UBERON:0000490!4.28e-13!138;UBERON:0001981!6.48e-13!60;UBERON:0007500!6.48e-13!60;UBERON:0004537!6.48e-13!60;UBERON:0006965!6.48e-13!60;UBERON:0004290!6.62e-13!70;UBERON:0000926!7.40e-13!448;UBERON:0004120!7.40e-13!448;UBERON:0006603!7.40e-13!448;UBERON:0002049!1.12e-12!79;UBERON:0007798!1.12e-12!79;UBERON:0001637!1.21e-12!42;UBERON:0003509!1.21e-12!42;UBERON:0004572!1.21e-12!42;UBERON:0000055!2.51e-12!69;UBERON:0000119!4.69e-12!312;UBERON:0000483!6.64e-12!309;UBERON:0001134!1.95e-11!61;UBERON:0002036!1.95e-11!61;UBERON:0003082!1.95e-11!61;UBERON:0002385!2.64e-11!63;UBERON:0001015!2.64e-11!63;UBERON:0000383!2.64e-11!63;UBERON:0001009!3.59e-11!113;UBERON:0004573!6.91e-11!33;UBERON:0004571!6.91e-11!33;UBERON:0004535!7.01e-11!110;UBERON:0000481!2.14e-10!347;UBERON:0000477!6.16e-10!286;UBERON:0000922!8.19e-09!612;UBERON:0002050!9.54e-09!605;UBERON:0005423!9.54e-09!605;UBERON:0000923!9.59e-09!604;UBERON:0005291!9.59e-09!604;UBERON:0006598!9.59e-09!604;UBERON:0002532!9.59e-09!604;UBERON:0001048!1.33e-08!168;UBERON:0004111!1.90e-08!241;UBERON:0004923!6.15e-08!57;UBERON:0003102!1.00e-07!95;UBERON:0009569!2.25e-07!113;UBERON:0001013!2.70e-07!14;UBERON:0002199!2.80e-07!45;UBERON:0002416!2.80e-07!45;UBERON:0000947!2.99e-07!21;UBERON:0010191!2.99e-07!21;UBERON:0000025!5.18e-07!194;UBERON:0000466!5.45e-07!126
|ontology_enrichment_uberon=UBERON:0003914!5.49e-19!117;UBERON:0002100!1.37e-17!199;UBERON:0000475!1.04e-16!264;UBERON:0000468!2.30e-16!656;UBERON:0004872!5.13e-16!83;UBERON:0005256!5.28e-16!122;UBERON:0003104!8.88e-15!160;UBERON:0009142!8.88e-15!160;UBERON:0007503!1.37e-14!78;UBERON:0000490!3.58e-14!148;UBERON:0000486!1.88e-13!83;UBERON:0000467!3.37e-13!624;UBERON:0000480!4.96e-13!625;UBERON:0002329!1.04e-12!71;UBERON:0003059!1.04e-12!71;UBERON:0007282!1.04e-12!71;UBERON:0004290!1.04e-12!71;UBERON:0009618!1.04e-12!71;UBERON:0007524!1.25e-12!73;UBERON:0001637!2.22e-12!42;UBERON:0003509!2.22e-12!42;UBERON:0004572!2.22e-12!42;UBERON:0003077!2.77e-12!72;UBERON:0007285!2.77e-12!72;UBERON:0002049!3.34e-12!78;UBERON:0007798!3.34e-12!78;UBERON:0007500!6.48e-12!59;UBERON:0001981!6.48e-12!59;UBERON:0004537!6.48e-12!59;UBERON:0006965!6.48e-12!59;UBERON:0000119!9.36e-12!309;UBERON:0000055!1.38e-11!68;UBERON:0000483!1.50e-11!306;UBERON:0001134!3.07e-11!62;UBERON:0002036!3.07e-11!62;UBERON:0003082!3.07e-11!62;UBERON:0002385!4.45e-11!64;UBERON:0001015!4.45e-11!64;UBERON:0000383!4.45e-11!64;UBERON:0001009!7.58e-11!112;UBERON:0004535!1.42e-10!109;UBERON:0004573!1.46e-10!33;UBERON:0004571!1.46e-10!33;UBERON:0000481!3.11e-09!342;UBERON:0001048!1.32e-08!160;UBERON:0004923!1.68e-08!66;UBERON:0004111!6.00e-08!240;UBERON:0000926!1.09e-07!315;UBERON:0004120!1.09e-07!315;UBERON:0006603!1.09e-07!315;UBERON:0003102!1.57e-07!99;UBERON:0001013!2.22e-07!14;UBERON:0002199!2.36e-07!46;UBERON:0002416!2.36e-07!46;UBERON:0000477!2.95e-07!373;UBERON:0000947!3.35e-07!21;UBERON:0010191!3.35e-07!21;UBERON:0009569!5.53e-07!112
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513063769880585!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.010665511845783!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101577950049047!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.00154718249563033!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.018641004886611!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248457666279866!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088865326243996!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241995158806951!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322832401388278!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.00097081729668445!TBP#6908;4:3.70677068709639:0.00529637781478435:0.024469096814928!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249453142214089
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}}
}}

Revision as of 14:20, 19 October 2012


Full id: C2716_Osteoblast_leiomyoma_Preadipocyte_Adipocyte_mesenchymal_Smooth_Mesothelial



Phase1 CAGE Peaks

Hg19::chr3:124606049..124606060,-p9@ITGB5
Hg19::chr3:124606074..124606198,-p1@ITGB5
Hg19::chr3:124606201..124606223,-p2@ITGB5
Hg19::chr3:124606225..124606243,-p6@ITGB5


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
epithelial tube5.49e-19117
trunk1.37e-17199
organism subdivision1.04e-16264
multi-cellular organism2.30e-16656
splanchnic layer of lateral plate mesoderm5.13e-1683
trunk mesenchyme5.28e-16122
mesenchyme8.88e-15160
entire embryonic mesenchyme8.88e-15160
epithelial vesicle1.37e-1478
unilaminar epithelium3.58e-14148
multilaminar epithelium1.88e-1383
anatomical system3.37e-13624
anatomical group4.96e-13625
somite1.04e-1271
presomitic mesoderm1.04e-1271
presumptive segmental plate1.04e-1271
dermomyotome1.04e-1271
trunk paraxial mesoderm1.04e-1271
dense mesenchyme tissue1.25e-1273
artery2.22e-1242
arterial blood vessel2.22e-1242
arterial system2.22e-1242
paraxial mesoderm2.77e-1272
presumptive paraxial mesoderm2.77e-1272
vasculature3.34e-1278
vascular system3.34e-1278
epithelial tube open at both ends6.48e-1259
blood vessel6.48e-1259
blood vasculature6.48e-1259
vascular cord6.48e-1259
cell layer9.36e-12309
vessel1.38e-1168
epithelium1.50e-11306
skeletal muscle tissue3.07e-1162
striated muscle tissue3.07e-1162
myotome3.07e-1162
muscle tissue4.45e-1164
musculature4.45e-1164
musculature of body4.45e-1164
circulatory system7.58e-11112
cardiovascular system1.42e-10109
systemic artery1.46e-1033
systemic arterial system1.46e-1033
multi-tissue structure3.11e-09342
primordium1.32e-08160
organ component layer1.68e-0866
anatomical conduit6.00e-08240
mesoderm1.09e-07315
mesoderm-derived structure1.09e-07315
presumptive mesoderm1.09e-07315
surface structure1.57e-0799
adipose tissue2.22e-0714
integument2.36e-0746
integumental system2.36e-0746
anatomical cluster2.95e-07373
aorta3.35e-0721
aortic system3.35e-0721
subdivision of trunk5.53e-07112


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#90546.336201576962630.0006203100587215640.00513063769880585
E2F1#186944.907389214879320.001724022357361790.010665511845783
EGR1#195844.988179094810140.001615011500076050.0101577950049047
ETS1#211349.728760922202340.0001115955317418140.00154718249563033
HEY1#2346244.040111043105710.00375304636917980.018641004886611
HMGN3#932448.178547723350590.0002234570284440470.00248457666279866
MYC#460945.22228187160940.001344309395272740.0088865326243996
SMARCB1#6598418.25271578115749.00423392720929e-060.000241995158806951
TAF1#687243.343046285745290.008005664898701650.0322832401388278
TAF7#6879411.43306940492395.85061525419808e-050.00097081729668445
TBP#690843.706770687096390.005296377814784350.024469096814928
ZNF263#1012748.221841637010680.0002187871180958320.00249453142214089



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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