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Coexpression cluster:C4207: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!1.45e-24!83;UBERON:0002329!1.45e-24!83;UBERON:0003077!1.45e-24!83;UBERON:0003059!1.45e-24!83;UBERON:0007282!1.45e-24!83;UBERON:0009618!1.45e-24!83;UBERON:0007285!1.45e-24!83;UBERON:0004290!3.11e-22!70;UBERON:0000486!2.49e-20!82;UBERON:0003102!5.69e-19!95;UBERON:0001134!1.15e-17!61;UBERON:0002036!1.15e-17!61;UBERON:0003082!1.15e-17!61;UBERON:0002385!1.28e-17!63;UBERON:0001015!1.28e-17!63;UBERON:0000383!1.28e-17!63;UBERON:0002199!9.50e-15!45;UBERON:0002416!9.50e-15!45;UBERON:0000475!3.30e-14!365;UBERON:0005256!1.06e-13!143;UBERON:0000468!9.03e-13!659;UBERON:0002097!4.79e-12!40;UBERON:0000467!5.41e-12!625;UBERON:0000480!9.55e-12!626;UBERON:0002100!1.06e-11!216;UBERON:0004872!1.22e-11!84;UBERON:0001637!6.32e-11!42;UBERON:0003509!6.32e-11!42;UBERON:0004572!6.32e-11!42;UBERON:0000481!1.56e-09!347;UBERON:0003104!1.74e-09!238;UBERON:0009142!1.74e-09!238;UBERON:0001013!2.02e-09!14;UBERON:0004573!2.02e-09!33;UBERON:0004571!2.02e-09!33;UBERON:0001981!4.35e-09!60;UBERON:0007500!4.35e-09!60;UBERON:0004537!4.35e-09!60;UBERON:0006965!4.35e-09!60;UBERON:0002049!5.31e-09!79;UBERON:0007798!5.31e-09!79;UBERON:0000926!9.02e-09!448;UBERON:0004120!9.02e-09!448;UBERON:0006603!9.02e-09!448;UBERON:0000490!2.26e-08!138;UBERON:0000055!3.75e-07!69;UBERON:0002050!4.42e-07!605;UBERON:0005423!4.42e-07!605;UBERON:0004535!5.24e-07!110;UBERON:0001009!6.17e-07!113;UBERON:0000923!6.53e-07!604;UBERON:0005291!6.53e-07!604;UBERON:0006598!6.53e-07!604;UBERON:0002532!6.53e-07!604;UBERON:0000119!9.05e-07!312
|ontology_enrichment_uberon=UBERON:0000914!1.45e-24!83;UBERON:0002329!1.45e-24!83;UBERON:0003077!1.45e-24!83;UBERON:0003059!1.45e-24!83;UBERON:0007282!1.45e-24!83;UBERON:0009618!1.45e-24!83;UBERON:0007285!1.45e-24!83;UBERON:0004290!3.11e-22!70;UBERON:0000486!2.49e-20!82;UBERON:0003102!5.69e-19!95;UBERON:0001134!1.15e-17!61;UBERON:0002036!1.15e-17!61;UBERON:0003082!1.15e-17!61;UBERON:0002385!1.28e-17!63;UBERON:0001015!1.28e-17!63;UBERON:0000383!1.28e-17!63;UBERON:0002199!9.50e-15!45;UBERON:0002416!9.50e-15!45;UBERON:0000475!3.30e-14!365;UBERON:0005256!1.06e-13!143;UBERON:0000468!9.03e-13!659;UBERON:0002097!4.79e-12!40;UBERON:0000467!5.41e-12!625;UBERON:0000480!9.55e-12!626;UBERON:0002100!1.06e-11!216;UBERON:0004872!1.22e-11!84;UBERON:0001637!6.32e-11!42;UBERON:0003509!6.32e-11!42;UBERON:0004572!6.32e-11!42;UBERON:0000481!1.56e-09!347;UBERON:0003104!1.74e-09!238;UBERON:0009142!1.74e-09!238;UBERON:0001013!2.02e-09!14;UBERON:0004573!2.02e-09!33;UBERON:0004571!2.02e-09!33;UBERON:0001981!4.35e-09!60;UBERON:0007500!4.35e-09!60;UBERON:0004537!4.35e-09!60;UBERON:0006965!4.35e-09!60;UBERON:0002049!5.31e-09!79;UBERON:0007798!5.31e-09!79;UBERON:0000926!9.02e-09!448;UBERON:0004120!9.02e-09!448;UBERON:0006603!9.02e-09!448;UBERON:0000490!2.26e-08!138;UBERON:0000055!3.75e-07!69;UBERON:0002050!4.42e-07!605;UBERON:0005423!4.42e-07!605;UBERON:0004535!5.24e-07!110;UBERON:0001009!6.17e-07!113;UBERON:0000923!6.53e-07!604;UBERON:0005291!6.53e-07!604;UBERON:0006598!6.53e-07!604;UBERON:0002532!6.53e-07!604;UBERON:0000119!9.05e-07!312
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.011549525087793!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280217858438604!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326313459630847
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}}
}}

Revision as of 12:48, 5 September 2012


Full id: C4207_Mesenchymal_Fibroblast_Adipocyte_Pancreatic_Trabecular_tenocyte_Hair



Phase1 CAGE Peaks

Hg19::chr2:239756536..239756564,-p1@BC143627
Hg19::chr2:239756671..239756732,+p1@TWIST2
Hg19::chr2:239756739..239756755,+p2@TWIST2


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


GO IDGO nameFDR corrected p-value
GO:0045668negative regulation of osteoblast differentiation0.00868362180619333
GO:0045667regulation of osteoblast differentiation0.00868362180619333
GO:0001649osteoblast differentiation0.0144727030103222
GO:0045596negative regulation of cell differentiation0.0202617842144511
GO:0051093negative regulation of developmental process0.0202617842144511
GO:0001503ossification0.0202617842144511
GO:0031214biomineral formation0.0202617842144511
GO:0046849bone remodeling0.0202617842144511
GO:0048771tissue remodeling0.0202617842144511
GO:0045595regulation of cell differentiation0.0250088308018368
GO:0045892negative regulation of transcription, DNA-dependent0.0285891548696211
GO:0001501skeletal development0.0285891548696211
GO:0016564transcription repressor activity0.0285891548696211
GO:0050793regulation of developmental process0.0292762106608804
GO:0016481negative regulation of transcription0.0325891218373609
GO:0009888tissue development0.0325891218373609
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0325891218373609
GO:0031324negative regulation of cellular metabolic process0.0367606656462185
GO:0009892negative regulation of metabolic process0.039853253763161



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
somite1.45e-2483
paraxial mesoderm1.45e-2483
presomitic mesoderm1.45e-2483
presumptive segmental plate1.45e-2483
trunk paraxial mesoderm1.45e-2483
presumptive paraxial mesoderm1.45e-2483
dermomyotome3.11e-2270
multilaminar epithelium2.49e-2082
surface structure5.69e-1995
skeletal muscle tissue1.15e-1761
striated muscle tissue1.15e-1761
myotome1.15e-1761
muscle tissue1.28e-1763
musculature1.28e-1763
musculature of body1.28e-1763
integument9.50e-1545
integumental system9.50e-1545
organism subdivision3.30e-14365
trunk mesenchyme1.06e-13143
multi-cellular organism9.03e-13659
skin of body4.79e-1240
anatomical system5.41e-12625
anatomical group9.55e-12626
trunk1.06e-11216
splanchnic layer of lateral plate mesoderm1.22e-1184
artery6.32e-1142
arterial blood vessel6.32e-1142
arterial system6.32e-1142
multi-tissue structure1.56e-09347
mesenchyme1.74e-09238
entire embryonic mesenchyme1.74e-09238
adipose tissue2.02e-0914
systemic artery2.02e-0933
systemic arterial system2.02e-0933
blood vessel4.35e-0960
epithelial tube open at both ends4.35e-0960
blood vasculature4.35e-0960
vascular cord4.35e-0960
vasculature5.31e-0979
vascular system5.31e-0979
mesoderm9.02e-09448
mesoderm-derived structure9.02e-09448
presumptive mesoderm9.02e-09448
unilaminar epithelium2.26e-08138
vessel3.75e-0769
embryonic structure4.42e-07605
developing anatomical structure4.42e-07605
cardiovascular system5.24e-07110
circulatory system6.17e-07113
germ layer6.53e-07604
embryonic tissue6.53e-07604
presumptive structure6.53e-07604
epiblast (generic)6.53e-07604
cell layer9.05e-07312


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#105137.971147625824820.001974187055288560.011549525087793
CTCF#1066435.360256373075030.0064925092527670.0280217858438604
E2F1#186934.907389214879320.008460985347239390.0326313459630847



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.