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Coexpression cluster:C4027: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4027_Wilms_Endothelial_mesothelioma_Renal_mesenchymal_leiomyoma_Fibroblast
|id=C4027
}}

Latest revision as of 12:37, 17 September 2013


Full id: C4027_Wilms_Endothelial_mesothelioma_Renal_mesenchymal_leiomyoma_Fibroblast



Phase1 CAGE Peaks

Hg19::chr20:33759838..33759845,+p5@PROCR
Hg19::chr20:33759854..33759916,+p1@PROCR
Hg19::chr20:33759924..33759940,+p6@PROCR


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>

Cell Type
Ontology termp-valuen
mesodermal cell9.71e-24121
embryonic cell1.07e-18250
endothelial cell5.10e-1636
meso-epithelial cell6.43e-1645
endothelial cell of vascular tree1.91e-1524
lining cell9.01e-1458
barrier cell9.01e-1458
blood vessel endothelial cell3.49e-1318
embryonic blood vessel endothelial progenitor cell3.49e-1318
contractile cell3.53e-1159
muscle precursor cell6.41e-1158
myoblast6.41e-1158
multi-potent skeletal muscle stem cell6.41e-1158
epithelial cell1.34e-10253
muscle cell1.43e-1055
smooth muscle cell2.28e-0943
smooth muscle myoblast2.28e-0943
squamous epithelial cell2.95e-0963
non-terminally differentiated cell8.74e-09106
fibroblast9.78e-0976
electrically responsive cell1.75e-0861
electrically active cell1.75e-0861
vascular associated smooth muscle cell6.99e-0832
endothelial cell of artery1.19e-079
kidney cell5.11e-0717
kidney epithelial cell5.11e-0717
Uber Anatomy
Ontology termp-valuen
vasculature1.58e-2478
vascular system1.58e-2478
vessel2.36e-2468
epithelial tube open at both ends4.75e-2259
blood vessel4.75e-2259
blood vasculature4.75e-2259
vascular cord4.75e-2259
splanchnic layer of lateral plate mesoderm8.97e-2283
epithelial tube1.83e-20117
cardiovascular system1.95e-16109
circulatory system2.77e-16112
organism subdivision3.26e-16264
trunk2.48e-15199
artery5.04e-1542
arterial blood vessel5.04e-1542
arterial system5.04e-1542
unilaminar epithelium3.52e-14148
epithelial vesicle4.21e-1478
squamous epithelium1.39e-1325
blood vessel endothelium3.49e-1318
endothelium3.49e-1318
cardiovascular system endothelium3.49e-1318
simple squamous epithelium7.20e-1322
systemic artery8.06e-1333
systemic arterial system8.06e-1333
multilaminar epithelium1.34e-1283
multi-cellular organism6.85e-12656
mesenchyme2.00e-11160
entire embryonic mesenchyme2.00e-11160
somite3.21e-1171
presomitic mesoderm3.21e-1171
presumptive segmental plate3.21e-1171
dermomyotome3.21e-1171
trunk paraxial mesoderm3.21e-1171
skeletal muscle tissue3.48e-1162
striated muscle tissue3.48e-1162
myotome3.48e-1162
muscle tissue4.58e-1164
musculature4.58e-1164
musculature of body4.58e-1164
paraxial mesoderm1.10e-1072
presumptive paraxial mesoderm1.10e-1072
dense mesenchyme tissue1.35e-1073
cell layer3.25e-10309
anatomical system4.55e-10624
epithelium4.73e-10306
anatomical group7.51e-10625
trunk mesenchyme1.16e-09122
compound organ3.98e-0968
anatomical cluster6.98e-09373
aorta1.06e-0821
aortic system1.06e-0821
mesoderm4.20e-08315
mesoderm-derived structure4.20e-08315
presumptive mesoderm4.20e-08315
endothelial tube1.19e-079
arterial system endothelium1.19e-079
endothelium of artery1.19e-079
subdivision of trunk2.25e-07112
anatomical space3.41e-0795
body cavity precursor3.55e-0754


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
MA0017.10.686276
MA0019.10.990656
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
MA0061.10.456531
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
MA0088.12.03569
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.11.66081
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
MA0144.10.531867
MA0145.13.85295
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.12.04956
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.12.37721
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
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
FOS#235338.99795530889440.001372499272417130.00898529753099558
GATA1#2623313.56030814380040.0004009615963782630.00388316284904946
GATA2#2624312.7449317335540.0004829527704283790.00437232180918598
MAX#414936.452555509007120.003721913834265510.0186818358695081
SPI1#668838.204323508522730.001810593189410520.0109178142095176
STAT3#6774310.51946499715420.0008589184530415310.006432741793991
ZNF263#1012738.221841637010680.001799043925565870.0109569832366558



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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