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Coexpression cluster:C589: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;3:12.5434000678656:0.00159612266729121:0.0100541287846337!EGR1#1958;10:3.32545272987342:0.000115549638535482:0.00157154430251428!POLR2A#5430;15:2.14745317655807:1.04920735639056e-05:0.000272650328673983!RAD21#5885;6:4.14201355818253:0.00187629003014743:0.0110598179511552!ZBTB33#10009;3:6.33294500599623:0.0107732645418473:0.0397551047800859!ZNF263#10127;7:3.83685943060498:0.00103612939564987:0.00732798252537932
|tf_chipseq_enrich=CTBP2#1488;3:12.5434000678656:0.00159612266729121:0.0100541287846337!EGR1#1958;10:3.32545272987342:0.000115549638535482:0.00157154430251428!POLR2A#5430;15:2.14745317655807:1.04920735639056e-05:0.000272650328673983!RAD21#5885;6:4.14201355818253:0.00187629003014743:0.0110598179511552!ZBTB33#10009;3:6.33294500599623:0.0107732645418473:0.0397551047800859!ZNF263#10127;7:3.83685943060498:0.00103612939564987:0.00732798252537932
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}}
}}

Revision as of 14:19, 26 November 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
epithelial vesicle1.62e-2278
dense mesenchyme tissue2.20e-2273
somite4.45e-2271
presomitic mesoderm4.45e-2271
presumptive segmental plate4.45e-2271
dermomyotome4.45e-2271
trunk paraxial mesoderm4.45e-2271
paraxial mesoderm8.88e-2272
presumptive paraxial mesoderm8.88e-2272
multilaminar epithelium1.85e-2083
mesenchyme2.14e-20160
entire embryonic mesenchyme2.14e-20160
skeletal muscle tissue3.15e-2062
striated muscle tissue3.15e-2062
myotome3.15e-2062
muscle tissue5.75e-2064
musculature5.75e-2064
musculature of body5.75e-2064
trunk mesenchyme2.97e-18122
splanchnic layer of lateral plate mesoderm2.92e-1783
multi-cellular organism1.33e-16656
multi-tissue structure2.30e-16342
organism subdivision1.30e-15264
vasculature2.77e-1578
vascular system2.77e-1578
unilaminar epithelium8.60e-15148
cell layer2.21e-14309
anatomical cluster3.54e-14373
epithelial tube3.63e-14117
epithelium5.38e-14306
artery6.21e-1442
arterial blood vessel6.21e-1442
arterial system6.21e-1442
trunk9.32e-14199
epithelial tube open at both ends3.02e-1359
blood vessel3.02e-1359
blood vasculature3.02e-1359
vascular cord3.02e-1359
anatomical system8.50e-13624
anatomical group1.38e-12625
vessel1.87e-1268
systemic artery3.58e-1233
systemic arterial system3.58e-1233
circulatory system1.96e-11112
cardiovascular system2.59e-11109
anatomical conduit1.67e-08240
surface structure3.20e-0899
developing anatomical structure7.81e-08581
embryo8.41e-08592
embryonic structure1.05e-07564
germ layer1.40e-07560
germ layer / neural crest1.40e-07560
embryonic tissue1.40e-07560
presumptive structure1.40e-07560
germ layer / neural crest derived structure1.40e-07560
epiblast (generic)1.40e-07560
heart1.66e-0724
primitive heart tube1.66e-0724
primary heart field1.66e-0724
anterior lateral plate mesoderm1.66e-0724
heart tube1.66e-0724
heart primordium1.66e-0724
cardiac mesoderm1.66e-0724
cardiogenic plate1.66e-0724
heart rudiment1.66e-0724
integument1.86e-0746
integumental system1.86e-0746
primary circulatory organ2.22e-0727
tube3.78e-07192
aorta8.41e-0721
aortic system8.41e-0721


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#1488312.54340006786560.001596122667291210.0100541287846337
EGR1#1958103.325452729873420.0001155496385354820.00157154430251428
POLR2A#5430152.147453176558071.04920735639056e-050.000272650328673983
RAD21#588564.142013558182530.001876290030147430.0110598179511552
ZBTB33#1000936.332945005996230.01077326454184730.0397551047800859
ZNF263#1012773.836859430604980.001036129395649870.00732798252537932



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.