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Coexpression cluster:C1353: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;2:20.905666779776:0.00365309513216369:0.018450798070802!CTCF#10664;5:4.46688031089586:0.00114484834617236:0.00783479565073684!EGR1#1958;5:4.15681591234178:0.00161796681886444:0.0101300183799163!ELF1#1997;5:3.54841496567295:0.00344683777572169:0.0175243058348066!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380011212720019!SMC3#9126;3:7.52246642246642:0.00503954071682855:0.0234809097891973!TAF1#6872;5:2.78587190478774:0.0107863634029041:0.0397865722764674
|tf_chipseq_enrich=CTBP2#1488;2:20.905666779776:0.00365309513216369:0.018450798070802!CTCF#10664;5:4.46688031089586:0.00114484834617236:0.00783479565073684!EGR1#1958;5:4.15681591234178:0.00161796681886444:0.0101300183799163!ELF1#1997;5:3.54841496567295:0.00344683777572169:0.0175243058348066!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380011212720019!SMC3#9126;3:7.52246642246642:0.00503954071682855:0.0234809097891973!TAF1#6872;5:2.78587190478774:0.0107863634029041:0.0397865722764674
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}}
}}

Revision as of 14:50, 26 November 2012


Full id: C1353_Mesenchymal_Preadipocyte_basal_Adipocyte_Fibroblast_Smooth_leiomyoma



Phase1 CAGE Peaks

Hg19::chr11:844406..844448,+p4@TSPAN4
Hg19::chr19:42463447..42463513,-p1@RABAC1
Hg19::chr20:35169885..35169911,+p2@MYL9
Hg19::chr22:31503490..31503584,-p1@SELM
Hg19::chr22:43045336..43045416,-p1@CYB5R3
Hg19::chr22:43045417..43045424,-p6@CYB5R3


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 vesicle1.55e-2378
mesenchyme2.47e-21160
entire embryonic mesenchyme2.47e-21160
dense mesenchyme tissue3.48e-2173
somite4.38e-2171
presomitic mesoderm4.38e-2171
presumptive segmental plate4.38e-2171
dermomyotome4.38e-2171
trunk paraxial mesoderm4.38e-2171
paraxial mesoderm1.18e-2072
presumptive paraxial mesoderm1.18e-2072
splanchnic layer of lateral plate mesoderm1.45e-2083
vasculature4.01e-2078
vascular system4.01e-2078
multilaminar epithelium7.54e-2083
skeletal muscle tissue7.65e-2062
striated muscle tissue7.65e-2062
myotome7.65e-2062
muscle tissue9.62e-2064
musculature9.62e-2064
musculature of body9.62e-2064
trunk mesenchyme4.40e-19122
epithelial tube6.53e-18117
vessel1.25e-1768
epithelial tube open at both ends8.64e-1759
blood vessel8.64e-1759
blood vasculature8.64e-1759
vascular cord8.64e-1759
organism subdivision1.01e-16264
artery2.88e-1642
arterial blood vessel2.88e-1642
arterial system2.88e-1642
unilaminar epithelium6.33e-16148
multi-cellular organism7.08e-16656
circulatory system7.19e-16112
trunk8.99e-16199
cardiovascular system1.18e-15109
cell layer1.63e-15309
epithelium3.96e-15306
multi-tissue structure1.40e-14342
systemic artery2.12e-1333
systemic arterial system2.12e-1333
anatomical system1.16e-12624
anatomical group1.43e-12625
anatomical cluster6.97e-12373
anatomical conduit1.77e-10240
mesoderm3.49e-10315
mesoderm-derived structure3.49e-10315
presumptive mesoderm3.49e-10315
surface structure7.77e-0999
tube6.78e-08192
compound organ1.01e-0768
developing anatomical structure1.42e-07581
aorta1.93e-0721
aortic system1.93e-0721
embryo2.20e-07592
primary circulatory organ3.42e-0727
integument3.60e-0746
integumental system3.60e-0746
heart3.81e-0724
primitive heart tube3.81e-0724
primary heart field3.81e-0724
anterior lateral plate mesoderm3.81e-0724
heart tube3.81e-0724
heart primordium3.81e-0724
cardiac mesoderm3.81e-0724
cardiogenic plate3.81e-0724
heart rudiment3.81e-0724
embryonic structure7.55e-07564


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
CTBP2#1488220.9056667797760.003653095132163690.018450798070802
CTCF#1066454.466880310895860.001144848346172360.00783479565073684
EGR1#195854.156815912341780.001617966818864440.0101300183799163
ELF1#199753.548414965672950.003446837775721690.0175243058348066
POLR2A#543062.147453176558070.01019570676818780.0380011212720019
SMC3#912637.522466422466420.005039540716828550.0234809097891973
TAF1#687252.785871904787740.01078636340290410.0397865722764674



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.