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Coexpression cluster:C3791: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003102!2.40e-14!95;UBERON:0000914!1.71e-09!83;UBERON:0002329!1.71e-09!83;UBERON:0003077!1.71e-09!83;UBERON:0003059!1.71e-09!83;UBERON:0007282!1.71e-09!83;UBERON:0009618!1.71e-09!83;UBERON:0007285!1.71e-09!83;UBERON:0001444!1.86e-09!48;UBERON:0002199!3.47e-07!45;UBERON:0002416!3.47e-07!45;UBERON:0005256!9.99e-07!143
|ontology_enrichment_uberon=UBERON:0003102!2.40e-14!95;UBERON:0000914!1.71e-09!83;UBERON:0002329!1.71e-09!83;UBERON:0003077!1.71e-09!83;UBERON:0003059!1.71e-09!83;UBERON:0007282!1.71e-09!83;UBERON:0009618!1.71e-09!83;UBERON:0007285!1.71e-09!83;UBERON:0001444!1.86e-09!48;UBERON:0002199!3.47e-07!45;UBERON:0002416!3.47e-07!45;UBERON:0005256!9.99e-07!143
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189995650939626!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322145961515452!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00762021592725895!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108682618807042!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128042747192625!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199578708956838!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245780002592121!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136622858949207!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246423813737989!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000939880721739887!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109064795310212!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613598775233761!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.014015746442241
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}}
}}

Revision as of 12:07, 5 September 2012


Full id: C3791_Mesenchymal_Trabecular_Fibroblast_Prostate_Smooth_Nucleus_sacrococcigeal



Phase1 CAGE Peaks

Hg19::chr19:41119794..41119844,+p6@LTBP4
Hg19::chr19:41119846..41119862,+p7@LTBP4
Hg19::chr19:41120037..41120121,+p2@LTBP4


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell4.48e-12180
fibroblast7.54e-1275
somatic cell5.39e-10591
contractile cell4.97e-0959
smooth muscle cell6.61e-0942
smooth muscle myoblast6.61e-0942
muscle cell5.57e-0854
Uber Anatomy
Ontology termp-valuen
surface structure2.40e-1495
somite1.71e-0983
paraxial mesoderm1.71e-0983
presomitic mesoderm1.71e-0983
presumptive segmental plate1.71e-0983
trunk paraxial mesoderm1.71e-0983
presumptive paraxial mesoderm1.71e-0983
subdivision of head1.86e-0948
integument3.47e-0745
integumental system3.47e-0745
trunk mesenchyme9.99e-07143


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#90536.336201576962630.003930750035764890.0189995650939626
E2F6#187635.017155731697390.00791769806886330.0322145961515452
ETS1#211339.728760922202340.001085840092584840.00762021592725895
HMGN3#932438.178547723350590.001827766942164210.0108682618807042
IRF1#365937.63716375356390.002244692747297240.0128042747192625
NFYA#4800318.42558069983050.0001598135507814160.00199578708956838
NFYB#4801316.75979325353650.0002123649923296180.00245780002592121
PBX3#5090321.91451268674419.49854535978121e-050.00136622858949207
SP1#666735.69838137814090.005403962701712170.0246423813737989
SP2#6668326.15353049384465.58768218891694e-050.000939880721739887
SPI1#668838.204323508522730.001810593189410520.0109064795310212
TCF7L2#6934310.77017656313730.0008003181298398380.00613598775233761
ZBTB7A#5134137.35190930787590.002516255860282270.014015746442241



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.