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{{Coexpression_clusters
{
|full_id=C4257_Endothelial_basal_Smooth_bone_Renal_mesenchymal_Fibroblast
 

Latest revision as of 12:42, 17 September 2013


Full id: C4257_Endothelial_basal_Smooth_bone_Renal_mesenchymal_Fibroblast



Phase1 CAGE Peaks

Hg19::chr3:104628747..104628762,-p@chr3:104628747..104628762
-
Hg19::chr4:86699902..86699958,+p4@ARHGAP24
Hg19::chr4:86699968..86699983,+p11@ARHGAP24


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 cell2.76e-28121
endothelial cell of vascular tree5.42e-2724
endothelial cell6.32e-2336
blood vessel endothelial cell8.79e-2118
embryonic blood vessel endothelial progenitor cell8.79e-2118
meso-epithelial cell2.54e-1845
lining cell1.93e-1758
barrier cell1.93e-1758
fibroblast2.61e-1376
muscle precursor cell2.85e-1358
myoblast2.85e-1358
multi-potent skeletal muscle stem cell2.85e-1358
skin fibroblast2.74e-1223
endothelial cell of artery1.81e-119
muscle cell3.09e-1155
contractile cell1.62e-1059
smooth muscle cell1.28e-0943
smooth muscle myoblast1.28e-0943
electrically responsive cell4.05e-0961
electrically active cell4.05e-0961
embryonic cell4.34e-09250
vascular associated smooth muscle cell2.13e-0832
aortic endothelial cell3.80e-086
vein endothelial cell3.85e-086
lymphangioblast9.39e-086
endothelial cell of lymphatic vessel9.39e-086
vascular lymphangioblast9.39e-086
somatic cell3.84e-07588
multi fate stem cell7.65e-07427
non-terminally differentiated cell8.07e-07106
Uber Anatomy
Ontology termp-valuen
vessel1.23e-3268
epithelial tube open at both ends3.10e-2959
blood vessel3.10e-2959
blood vasculature3.10e-2959
vascular cord3.10e-2959
vasculature8.54e-2778
vascular system8.54e-2778
splanchnic layer of lateral plate mesoderm1.12e-2683
artery1.20e-2142
arterial blood vessel1.20e-2142
arterial system1.20e-2142
epithelial tube3.80e-21117
blood vessel endothelium8.79e-2118
endothelium8.79e-2118
cardiovascular system endothelium8.79e-2118
cardiovascular system2.79e-20109
circulatory system6.32e-20112
unilaminar epithelium1.20e-19148
epithelial vesicle4.17e-1978
squamous epithelium3.44e-1725
simple squamous epithelium3.78e-1722
somite1.18e-1671
presomitic mesoderm1.18e-1671
presumptive segmental plate1.18e-1671
dermomyotome1.18e-1671
trunk paraxial mesoderm1.18e-1671
paraxial mesoderm3.30e-1672
presumptive paraxial mesoderm3.30e-1672
systemic artery7.07e-1633
systemic arterial system7.07e-1633
dense mesenchyme tissue8.91e-1673
mesoderm9.12e-15315
mesoderm-derived structure9.12e-15315
presumptive mesoderm9.12e-15315
multilaminar epithelium1.18e-1383
muscle tissue1.54e-1264
musculature1.54e-1264
musculature of body1.54e-1264
skeletal muscle tissue2.03e-1262
striated muscle tissue2.03e-1262
myotome2.03e-1262
trunk mesenchyme8.75e-12122
endothelial tube1.81e-119
arterial system endothelium1.81e-119
endothelium of artery1.81e-119
aorta4.86e-1121
aortic system4.86e-1121
integument1.81e-1046
integumental system1.81e-1046
skin of body2.46e-0941
mesenchyme9.49e-09160
entire embryonic mesenchyme9.49e-09160
trunk9.90e-09199
cell layer3.85e-08309
umbilical blood vessel5.55e-089
epithelium8.61e-08306
vein2.94e-079
venous blood vessel2.94e-079
venous system2.94e-079


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)
MA0003.10.0471418
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
MA0050.11.90116
MA0051.12.15619
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
MA0088.10.257905
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
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.12.18164
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.22.07011
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.12.08673
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
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
BATF#10538216.23853452820240.004917462407809970.023001381960286
BCL11A#53335218.91297006907140.003639406248379680.0183941129101106
FOS#235338.99795530889440.001372499272417130.00899714106904171
IRF4#3662214.60967512449610.006056122473217890.026850712131958



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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