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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.465820579842489,0

Latest revision as of 11:25, 17 September 2013


Full id: C566_Pericytes_Renal_hepatic_Fibroblast_Endothelial_Hepatic_Lens



Phase1 CAGE Peaks

Hg19::chr13:110802350..110802403,-p3@COL4A1
Hg19::chr13:110802503..110802522,-p9@COL4A1
Hg19::chr13:110802740..110802769,-p2@COL4A1
Hg19::chr13:110804802..110804837,-p@chr13:110804802..110804837
-
Hg19::chr13:110829310..110829326,-p@chr13:110829310..110829326
-
Hg19::chr13:110829341..110829354,-p@chr13:110829341..110829354
-
Hg19::chr13:110839601..110839634,-p@chr13:110839601..110839634
-
Hg19::chr13:110853822..110853836,-p@chr13:110853822..110853836
-
Hg19::chr13:110861222..110861235,-p@chr13:110861222..110861235
-
Hg19::chr13:110864247..110864268,-p@chr13:110864247..110864268
-
Hg19::chr13:110959496..110959511,-p1@COL4A1
Hg19::chr13:110959598..110959611,+p2@COL4A2
Hg19::chr13:110959623..110959640,+p1@COL4A2
Hg19::chr13:111009846..111009888,-p@chr13:111009846..111009888
-
Hg19::chr13:111164370..111164403,+p@chr13:111164370..111164403
+
Hg19::chr13:111164549..111164576,+p@chr13:111164549..111164576
+


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

p.valueFDRnGenesnPathwayName
4.88436109433595e-050.003864750715893322200Focal adhesion (KEGG):04510
8.76239653607e-060.00110931940146646285ECM-receptor interaction (KEGG):04512
7.95242710836606e-060.00110931940146646281Protein digestion and absorption (KEGG):04974
1.36590298944621e-050.001441027653865752106Amoebiasis (KEGG):05146
0.0001308247892910560.007528371965567112327Pathways in cancer (KEGG):05200
8.76239653607e-060.00110931940146646285Small cell lung cancer (KEGG):05222
4.31443715156972e-050.003864750715893322188Focal Adhesion (Wikipathways):WP306
8.76239653607e-060.00110931940146646285Integrin cell surface interactions (Reactome):REACT_13552
5.10526184734612e-060.00110931940146646265Signaling by PDGF (Reactome):REACT_16888
8.58567593366187e-050.006038592073342182265Axon guidance (Reactome):REACT_18266
0.0008161546487882360.04305215772357942816TGF beta receptor up reg. targets (Netpath):NetPath_7
0.0001014376257822690.006421001712017642288{ACTB,297} (Static Module):NA



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:0005581collagen9.1276660944864e-05
GO:0005604basement membrane9.1276660944864e-05
GO:0005201extracellular matrix structural constituent0.00013724278986645
GO:0044420extracellular matrix part0.00013724278986645
GO:0006817phosphate transport0.00013724278986645
GO:0015698inorganic anion transport0.000379277449588247
GO:0006820anion transport0.000502106119333132
GO:0005578proteinaceous extracellular matrix0.000746924249734859
GO:0005587collagen type IV0.00127548516830642
GO:0030935sheet-forming collagen0.00137750370557821
GO:0044421extracellular region part0.00254125210080381
GO:0016525negative regulation of angiogenesis0.003251912687054
GO:0006811ion transport0.00483283573650064
GO:0045765regulation of angiogenesis0.0062286291620965
GO:0030198extracellular matrix organization and biogenesis0.00703642914021911
GO:0043062extracellular structure organization and biogenesis0.0120393189222703
GO:0001525angiogenesis0.0173898289872081
GO:0048514blood vessel morphogenesis0.0181053237656383
GO:0048646anatomical structure formation0.0181053237656383
GO:0001568blood vessel development0.0181053237656383
GO:0001944vasculature development0.0181053237656383
GO:0006810transport0.0250029879971245
GO:0051234establishment of localization0.0251161640147931
GO:0051179localization0.0282668149955082
GO:0009887organ morphogenesis0.0330695538606439



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
vasculature2.70e-1778
vascular system2.70e-1778
epithelial tube2.79e-16117
circulatory system9.65e-16112
cardiovascular system5.00e-15109
splanchnic layer of lateral plate mesoderm6.64e-1483
vessel1.00e-1368
mesenchyme6.40e-13160
entire embryonic mesenchyme6.40e-13160
epithelial tube open at both ends1.87e-1059
blood vessel1.87e-1059
blood vasculature1.87e-1059
vascular cord1.87e-1059
trunk mesenchyme8.10e-10122
epithelial vesicle1.45e-0978
muscle tissue1.46e-0964
musculature1.46e-0964
musculature of body1.46e-0964
skeletal muscle tissue3.46e-0962
striated muscle tissue3.46e-0962
myotome3.46e-0962
trunk3.86e-09199
compound organ4.44e-0968
nephron epithelium1.53e-0815
renal tubule1.53e-0815
nephron tubule1.53e-0815
nephron1.53e-0815
uriniferous tubule1.53e-0815
nephrogenic mesenchyme1.53e-0815
excretory tube1.60e-0816
kidney epithelium1.60e-0816
parenchyma5.55e-0815
unilaminar epithelium9.02e-08148
organism subdivision1.43e-07264
mesoderm3.75e-07315
mesoderm-derived structure3.75e-07315
presumptive mesoderm3.75e-07315
artery5.77e-0742
arterial blood vessel5.77e-0742
arterial system5.77e-0742
dense mesenchyme tissue6.75e-0773
urogenital ridge6.85e-0711
cortex of kidney6.85e-0712
renal parenchyma6.85e-0712
somite7.35e-0771
presomitic mesoderm7.35e-0771
presumptive segmental plate7.35e-0771
dermomyotome7.35e-0771
trunk paraxial mesoderm7.35e-0771
abdominal segment of trunk8.28e-0760
abdomen8.28e-0760


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)
MA0003.10.357653
MA0004.10.238283
MA0006.10.392773
MA0007.10.223897
MA0009.10.644692
MA0014.10.0018064
MA0017.10.150184
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.859342
MA0040.10.570428
MA0041.10.252793
MA0042.10.646075
MA0043.10.644989
MA0046.10.634468
MA0048.10.0172925
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.970157
MA0056.10
MA0057.10.189848
MA0058.10.5014
MA0059.10.166682
MA0060.10.464905
MA0061.10.0461955
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.10.0313753
MA0069.12.58716
MA0070.10.620368
MA0071.10.787225
MA0072.10.616162
MA0073.13.49367e-07
MA0074.10.316991
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.166796
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.20753
MA0089.10
MA0090.10.189305
MA0091.10.240316
MA0092.10.607109
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.403202
MA0103.10.75875
MA0105.10.0621554
MA0106.10.355999
MA0107.10.285979
MA0108.20.492699
MA0109.10
MA0111.10.199239
MA0113.10.370073
MA0114.10.278245
MA0115.10.874839
MA0116.11.02034
MA0117.10.680135
MA0119.10.471628
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.11.61446
MA0136.10.327047
MA0139.10.652922
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.928804
MA0145.10.418252
MA0146.10.710894
MA0147.10.296651
MA0148.10.257816
MA0149.10.279141
MA0062.20.168482
MA0035.20.780994
MA0039.25.16129e-05
MA0138.21.83663
MA0002.20.196222
MA0137.20.848496
MA0104.20.462925
MA0047.20.345656
MA0112.20.0357356
MA0065.20.667633
MA0150.10.5439
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.820684
MA0155.10.204406
MA0156.10.140505
MA0157.10.442323
MA0158.10
MA0159.10.0884959
MA0160.10.26995
MA0161.10
MA0162.10.311763
MA0163.10.473291
MA0164.10.380804
MA0080.20.126365
MA0018.20.357181
MA0099.20.795134
MA0079.20.0163847
MA0102.21.16862
MA0258.10.242841
MA0259.10.640339
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

No analysis results for this cluster

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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