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{{Coexpression_clusters
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Latest revision as of 11:46, 17 September 2013


Full id: C1515_Endothelial_schwannoma_Renal_cerebellum_lung_heart_diaphragm



Phase1 CAGE Peaks

Hg19::chr3:34262215..34262222,+p@chr3:34262215..34262222
+
Hg19::chr6:76203218..76203267,-p2@FILIP1
Hg19::chr8:16424975..16425011,-p3@MSR1
Hg19::chr8:16425014..16425019,-p13@MSR1
Hg19::chr8:16425043..16425061,-p5@MSR1
Hg19::chr8:16425067..16425095,-p7@MSR1


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:0006898receptor-mediated endocytosis0.0301424702696338
GO:0005044scavenger receptor activity0.0301424702696338
GO:0005319lipid transporter activity0.0301424702696338
GO:0006817phosphate transport0.0309274304329055
GO:0010324membrane invagination0.0309274304329055
GO:0006897endocytosis0.0309274304329055
GO:0015698inorganic anion transport0.033439302955375
GO:0016044membrane organization and biogenesis0.033439302955375
GO:0006820anion transport0.0338056176982351



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
endothelial cell of vascular tree7.89e-6124
endothelial cell4.55e-5736
meso-epithelial cell2.18e-4445
blood vessel endothelial cell3.81e-3918
embryonic blood vessel endothelial progenitor cell3.81e-3918
lining cell4.98e-3358
barrier cell4.98e-3358
lymphangioblast4.17e-246
endothelial cell of lymphatic vessel4.17e-246
vascular lymphangioblast4.17e-246
endothelial cell of artery3.26e-209
mesodermal cell9.44e-17121
aortic endothelial cell6.73e-166
capillary endothelial cell4.65e-133
fenestrated cell7.35e-135
glomerular endothelial cell7.35e-135
endothelial cell of umbilical vein3.37e-123
squamous epithelial cell7.66e-1263
vein endothelial cell2.92e-106
glomerular cell3.41e-097
kidney corpuscule cell3.41e-097
thoracic aorta endothelial cell5.21e-092
embryonic cell4.53e-08250
epithelial cell3.33e-07253
Uber Anatomy
Ontology termp-valuen
blood vessel endothelium3.81e-3918
endothelium3.81e-3918
cardiovascular system endothelium3.81e-3918
simple squamous epithelium2.07e-3122
squamous epithelium3.11e-2725
vessel2.91e-2268
endothelial tube3.26e-209
arterial system endothelium3.26e-209
endothelium of artery3.26e-209
vasculature1.08e-1878
vascular system1.08e-1878
lymphatic vessel6.63e-188
lymph vasculature6.63e-188
lymphatic part of lymphoid system6.63e-188
lymphoid system3.53e-1410
microcirculatory vessel4.65e-133
endothelium of capillary4.65e-133
capillary4.65e-133
epithelial tube open at both ends7.29e-1359
blood vessel7.29e-1359
blood vasculature7.29e-1359
vascular cord7.29e-1359
cardiovascular system7.87e-12109
circulatory system2.26e-11112
anatomical conduit4.06e-11240
epithelial tube2.55e-09117
primitive nephron3.41e-097
renal glomerulus3.41e-097
renal corpuscle3.41e-097
glomerular capsule3.41e-097
metanephric mesenchyme3.41e-097
glomerular tuft3.41e-097
S-shaped body3.41e-097
renal vesicle3.41e-097
comma-shaped body3.41e-097
segment of aorta5.21e-092
thoracic aorta5.21e-092
splanchnic layer of lateral plate mesoderm4.32e-0883
mesonephric epithelium4.81e-088
mesonephric tubule4.81e-088
nephric duct4.81e-088
renal duct4.81e-088
mesonephric duct4.81e-088
pronephric duct4.81e-088
tube8.63e-08192
anatomical cluster9.58e-08373
umbilical vein1.75e-075
mesonephros3.78e-079
pronephros3.78e-079
nephrogenic cord3.78e-079
pronephric mesoderm3.78e-079
rostral part of nephrogenic cord3.78e-079
presumptive pronephric mesoderm3.78e-079
vein7.50e-079
venous blood vessel7.50e-079
venous system7.50e-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)
MA0003.10.00461978
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.491287
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.12.08744
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.737586
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.12.56931
MA0072.12.29768
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.13.14993
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.11.61362
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.21.3092
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.11.21643
MA0151.10
MA0152.11.52275
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.21.02158
MA0018.21.69036
MA0099.21.52352
MA0079.25.9246e-06
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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#235357.498296090745349.22669120642035e-050.00134359509607827
JUN#3725510.42735766028031.82465747415735e-050.000415537291634364



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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