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Coexpression cluster:C3083: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3083_Osteoblast_Synoviocyte_tenocyte_Adipocyte_Preadipocyte_Mesenchymal_Sertoli
|id=C3083
}}

Latest revision as of 12:18, 17 September 2013


Full id: C3083_Osteoblast_Synoviocyte_tenocyte_Adipocyte_Preadipocyte_Mesenchymal_Sertoli



Phase1 CAGE Peaks

Hg19::chr11:114167069..114167146,+p1@NNMT
Hg19::chr11:114167149..114167162,+p4@NNMT
Hg19::chr11:114167202..114167221,+p3@NNMT


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
mesenchyme9.39e-24160
entire embryonic mesenchyme9.39e-24160
trunk mesenchyme9.86e-23122
unilaminar epithelium3.59e-21148
epithelial vesicle2.68e-2078
somite4.97e-2071
presomitic mesoderm4.97e-2071
presumptive segmental plate4.97e-2071
dermomyotome4.97e-2071
trunk paraxial mesoderm4.97e-2071
epithelial tube5.40e-20117
paraxial mesoderm3.07e-1972
presumptive paraxial mesoderm3.07e-1972
dense mesenchyme tissue3.34e-1973
skeletal muscle tissue1.66e-1862
striated muscle tissue1.66e-1862
myotome1.66e-1862
muscle tissue2.19e-1864
musculature2.19e-1864
musculature of body2.19e-1864
trunk9.67e-18199
multilaminar epithelium4.14e-1783
splanchnic layer of lateral plate mesoderm3.31e-1683
organism subdivision1.35e-15264
vasculature2.35e-1578
vascular system2.35e-1578
epithelium6.77e-14306
cell layer1.01e-13309
multi-tissue structure1.74e-13342
vessel8.90e-1368
circulatory system2.55e-12112
cardiovascular system2.75e-12109
epithelial tube open at both ends9.88e-1259
blood vessel9.88e-1259
blood vasculature9.88e-1259
vascular cord9.88e-1259
artery4.38e-1042
arterial blood vessel4.38e-1042
arterial system4.38e-1042
multi-cellular organism7.40e-10656
anatomical cluster9.79e-10373
anatomical conduit3.07e-09240
anatomical system1.47e-08624
heart2.03e-0824
primitive heart tube2.03e-0824
primary heart field2.03e-0824
anterior lateral plate mesoderm2.03e-0824
heart tube2.03e-0824
heart primordium2.03e-0824
cardiac mesoderm2.03e-0824
cardiogenic plate2.03e-0824
heart rudiment2.03e-0824
anatomical group2.30e-08625
primary circulatory organ4.20e-0827
surface structure5.80e-0899
adipose tissue9.79e-0814
systemic artery1.09e-0733
systemic arterial system1.09e-0733
integument1.61e-0746
integumental system1.61e-0746
mesoderm1.67e-07315
mesoderm-derived structure1.67e-07315
presumptive mesoderm1.67e-07315
primordium5.49e-07160
tube6.01e-07192


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.11.64148
MA0019.12.26702
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.17.68498
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.12.25834
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.21.20011
MA0137.22.70092
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.15.05652
MA0154.13.19371
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CEBPB#105137.971147625824820.001974187055288560.0114928718989566
CTCF#1066435.360256373075030.0064925092527670.027825153836831
EP300#203336.77394172622320.003216880500103790.0166849315926867
NR3C1#2908314.9730233311730.0002978331194675480.00307852268052962
STAT1#6772320.70658749719920.0001125992441046670.00154408514378247
STAT3#6774310.51946499715420.0008589184530415310.00641480151009757
USF1#739136.361499277207960.00388404057290560.0189509606817887



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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