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Coexpression cluster:C589: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!2.22e-24!83;UBERON:0002329!2.22e-24!83;UBERON:0003077!2.22e-24!83;UBERON:0003059!2.22e-24!83;UBERON:0007282!2.22e-24!83;UBERON:0009618!2.22e-24!83;UBERON:0007285!2.22e-24!83;UBERON:0004290!1.36e-22!70;UBERON:0005256!4.13e-21!143;UBERON:0000486!8.16e-21!82;UBERON:0000475!8.83e-21!365;UBERON:0001134!1.19e-20!61;UBERON:0002036!1.19e-20!61;UBERON:0003082!1.19e-20!61;UBERON:0002385!1.85e-20!63;UBERON:0001015!1.85e-20!63;UBERON:0000383!1.85e-20!63;UBERON:0004872!4.63e-17!84;UBERON:0002100!1.58e-16!216;UBERON:0000481!7.81e-16!347;UBERON:0002049!1.12e-15!79;UBERON:0007798!1.12e-15!79;UBERON:0000468!3.39e-15!659;UBERON:0000119!2.44e-14!312;UBERON:0003914!2.56e-14!118;UBERON:0000483!6.22e-14!309;UBERON:0001637!9.88e-14!42;UBERON:0003509!9.88e-14!42;UBERON:0004572!9.88e-14!42;UBERON:0001981!1.70e-13!60;UBERON:0007500!1.70e-13!60;UBERON:0004537!1.70e-13!60;UBERON:0006965!1.70e-13!60;UBERON:0000490!1.00e-12!138;UBERON:0000055!1.37e-12!69;UBERON:0003104!2.99e-12!238;UBERON:0009142!2.99e-12!238;UBERON:0004573!4.89e-12!33;UBERON:0004571!4.89e-12!33;UBERON:0001009!2.95e-11!113;UBERON:0000477!4.27e-11!286;UBERON:0004535!4.54e-11!110;UBERON:0000467!7.48e-11!625;UBERON:0000480!1.17e-10!626;UBERON:0003102!7.45e-09!95;UBERON:0004111!2.06e-08!241;UBERON:0000922!3.49e-08!612;UBERON:0002050!5.02e-08!605;UBERON:0005423!5.02e-08!605;UBERON:0000923!7.45e-08!604;UBERON:0005291!7.45e-08!604;UBERON:0006598!7.45e-08!604;UBERON:0002532!7.45e-08!604;UBERON:0002199!1.45e-07!45;UBERON:0002416!1.45e-07!45;UBERON:0000948!1.63e-07!24;UBERON:0005498!1.63e-07!24;UBERON:0004140!1.63e-07!24;UBERON:0009881!1.63e-07!24;UBERON:0004141!1.63e-07!24;UBERON:0003084!1.63e-07!24;UBERON:0007005!1.63e-07!24;UBERON:0004139!1.63e-07!24;UBERON:0004291!1.63e-07!24;UBERON:0007100!1.75e-07!27;UBERON:0000025!2.86e-07!194;UBERON:0003103!7.80e-07!69
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}}
}}

Revision as of 20:33, 8 August 2012


Full id: C589_Mesenchymal_Smooth_Fibroblast_Osteoblast_tenocyte_Preadipocyte_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr11:6411670..6411723,+p1@SMPD1
Hg19::chr11:65640198..65640281,-p1@EFEMP2
Hg19::chr11:65640308..65640317,-p3@EFEMP2
Hg19::chr11:65640325..65640346,-p2@EFEMP2
Hg19::chr15:74218787..74218813,+p1@LOXL1
Hg19::chr16:4421841..4421855,+p1@VASN
Hg19::chr17:46115122..46115173,-p1@COPZ2
Hg19::chr17:60705021..60705044,+p1@MRC2
Hg19::chr17:60705055..60705066,+p3@MRC2
Hg19::chr17:60705074..60705088,+p2@MRC2
Hg19::chr22:20792089..20792119,-p1@SCARF2
Hg19::chr22:31503460..31503464,-p2@ENST00000469262
Hg19::chr22:31503467..31503487,-p1@ENST00000469262
Hg19::chr8:22446763..22446862,+p1@PDLIM2


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:0018277protein amino acid deamination0.0336747910043565
GO:0006685sphingomyelin catabolic process0.0449150536397031
GO:0004720protein-lysine 6-oxidase activity0.0449150536397031
GO:0004767sphingomyelin phosphodiesterase activity0.0449150536397031
GO:0007157heterophilic cell adhesion0.0449150536397031
GO:0005801cis-Golgi network0.0449150536397031
GO:0009395phospholipid catabolic process0.0449150536397031
GO:0006684sphingomyelin metabolic process0.0449150536397031
GO:0030126COPI vesicle coat0.0449150536397031
GO:0030663COPI coated vesicle membrane0.0449150536397031
GO:0030149sphingolipid catabolic process0.0449150536397031
GO:0030137COPI-coated vesicle0.0449150536397031
GO:0005578proteinaceous extracellular matrix0.0449150536397031



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
somite2.22e-2483
paraxial mesoderm2.22e-2483
presomitic mesoderm2.22e-2483
presumptive segmental plate2.22e-2483
trunk paraxial mesoderm2.22e-2483
presumptive paraxial mesoderm2.22e-2483
dermomyotome1.36e-2270
trunk mesenchyme4.13e-21143
multilaminar epithelium8.16e-2182
organism subdivision8.83e-21365
skeletal muscle tissue1.19e-2061
striated muscle tissue1.19e-2061
myotome1.19e-2061
muscle tissue1.85e-2063
musculature1.85e-2063
musculature of body1.85e-2063
splanchnic layer of lateral plate mesoderm4.63e-1784
trunk1.58e-16216
multi-tissue structure7.81e-16347
vasculature1.12e-1579
vascular system1.12e-1579
multi-cellular organism3.39e-15659
cell layer2.44e-14312
epithelial tube2.56e-14118
epithelium6.22e-14309
artery9.88e-1442
arterial blood vessel9.88e-1442
arterial system9.88e-1442
blood vessel1.70e-1360
epithelial tube open at both ends1.70e-1360
blood vasculature1.70e-1360
vascular cord1.70e-1360
unilaminar epithelium1.00e-12138
vessel1.37e-1269
mesenchyme2.99e-12238
entire embryonic mesenchyme2.99e-12238
systemic artery4.89e-1233
systemic arterial system4.89e-1233
circulatory system2.95e-11113
anatomical cluster4.27e-11286
cardiovascular system4.54e-11110
anatomical system7.48e-11625
anatomical group1.17e-10626
surface structure7.45e-0995
anatomical conduit2.06e-08241
embryo3.49e-08612
embryonic structure5.02e-08605
developing anatomical structure5.02e-08605
germ layer7.45e-08604
embryonic tissue7.45e-08604
presumptive structure7.45e-08604
epiblast (generic)7.45e-08604
integument1.45e-0745
integumental system1.45e-0745
heart1.63e-0724
primitive heart tube1.63e-0724
primary heart field1.63e-0724
anterior lateral plate mesoderm1.63e-0724
heart tube1.63e-0724
heart primordium1.63e-0724
cardiac mesoderm1.63e-0724
cardiogenic plate1.63e-0724
heart rudiment1.63e-0724
primary circulatory organ1.75e-0727
tube2.86e-07194
compound organ7.80e-0769


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)

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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


No analysis results for this cluster

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.