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Coexpression cluster:C589: Difference between revisions

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{{Coexpression_clusters
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amino acid deamination!0.0336747910043565!4016$GO:0006685!sphingomyelin catabolic process!0.0449150536397031!6609$GO:0004720!protein-lysine 6-oxidase activity!0.0449150536397031!4016$GO:0004767!sphingomyelin phosphodiesterase activity!0.0449150536397031!6609$GO:0007157!heterophilic cell adhesion!0.0449150536397031!91179$GO:0005801!cis-Golgi network!0.0449150536397031!51226$GO:0009395!phospholipid catabolic process!0.0449150536397031!6609$GO:0006684!sphingomyelin metabolic process!0.0449150536397031!6609$GO:0030126!COPI vesicle coat!0.0449150536397031!51226$GO:0030663!COPI coated vesicle membrane!0.0449150536397031!51226$GO:0030149!sphingolipid catabolic process!0.0449150536397031!6609$GO:0030137!COPI-coated vesicle!0.0449150536397031!51226$GO:0005578!proteinaceous extracellular 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|full_id=C589_Mesenchymal_Smooth_Fibroblast_Osteoblast_tenocyte_Preadipocyte_Synoviocyte
|id=C589
}}

Latest revision as of 11:26, 17 September 2013


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)
MA0003.112.7815
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.14.69477
MA0017.10.494446
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.454219
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.441458
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.382722
MA0056.10
MA0057.10.688135
MA0058.10.538866
MA0059.10.182001
MA0060.10.0671843
MA0061.10.198509
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.0373092
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.11.07855
MA0074.10.337035
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.536866
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.12.0778
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.10.647316
MA0093.10.431889
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.437519
MA0103.10.131472
MA0105.12.65495
MA0106.10.37688
MA0107.10.650533
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.30732
MA0115.10.900969
MA0116.12.86257
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.11.10476
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.11.01483
MA0144.10.0838502
MA0145.12.7141
MA0146.14.33446
MA0147.10.326612
MA0148.10.276339
MA0149.10.298252
MA0062.20.745766
MA0035.20.305721
MA0039.23.79211
MA0138.21.91075
MA0002.21.25767
MA0137.20.153033
MA0104.20.874098
MA0047.20.366327
MA0112.20.988185
MA0065.21.06382
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.12.12649
MA0155.17.92071
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.12.89698
MA0160.10.786431
MA0161.10
MA0162.15.10278
MA0163.14.82149
MA0164.10.402162
MA0080.20.139746
MA0018.20.378086
MA0099.20.312108
MA0079.222.5391
MA0102.21.1957
MA0258.10.964206
MA0259.10.340204
MA0442.10



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.

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