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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.429123930638792,0

Latest revision as of 11:30, 17 September 2013


Full id: C750_Smooth_Mesenchymal_Fibroblast_Hepatic_Chondrocyte_Lens_tenocyte



Phase1 CAGE Peaks

Hg19::chr12:6937564..6937585,+p1@LEPREL2
Hg19::chr17:39968182..39968244,-p1@LEPREL4
Hg19::chr17:39968926..39968976,+p2@FKBP10
Hg19::chr17:39969232..39969265,+p1@FKBP10
Hg19::chr19:50031252..50031285,+p1@RCN3
Hg19::chr19:50031567..50031632,+p2@RCN3
Hg19::chr1:11994715..11994833,+p1@PLOD1
Hg19::chr1:12014885..12014920,+p@chr1:12014885..12014920
+
Hg19::chr1:43232649..43232715,-p1@LEPRE1
Hg19::chr7:150929550..150929619,+p1@CHPF2
Hg19::chrX:51636712..51636759,+p1@MAGED1


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:0031418L-ascorbic acid binding6.16739262198812e-07
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors2.05166582405436e-06
GO:0019797procollagen-proline 3-dioxygenase activity2.05166582405436e-06
GO:0031544peptidyl-proline 3-dioxygenase activity2.05166582405436e-06
GO:0005783endoplasmic reticulum2.05166582405436e-06
GO:0051213dioxygenase activity4.09714468760063e-06
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen4.09714468760063e-06
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen4.09714468760063e-06
GO:0019798procollagen-proline dioxygenase activity5.67381898068508e-06
GO:0031543peptidyl-proline dioxygenase activity7.14845068613665e-06
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen3.27411397309372e-05
GO:0019842vitamin binding7.96121713291799e-05
GO:0005788endoplasmic reticulum lumen0.00052552777865081
GO:0005506iron ion binding0.000584123997613624
GO:0044432endoplasmic reticulum part0.000601781767003522
GO:0005737cytoplasm0.000932935717654791
GO:0046946hydroxylysine metabolic process0.00128537226735743
GO:0046947hydroxylysine biosynthetic process0.00128537226735743
GO:0044444cytoplasmic part0.00165350468860902
GO:0008475procollagen-lysine 5-dioxygenase activity0.00346999433782819
GO:0008285negative regulation of cell proliferation0.00401542118850137
GO:0043169cation binding0.00767490924381294
GO:0046872metal ion binding0.00938806226834687
GO:0016491oxidoreductase activity0.00938806226834687
GO:0043167ion binding0.00938806226834687
GO:0030867rough endoplasmic reticulum membrane0.00978140308676731
GO:0050680negative regulation of epithelial cell proliferation0.0102746571907546
GO:0042127regulation of cell proliferation0.0128654976873371
GO:0009067aspartate family amino acid biosynthetic process0.0130046817132735
GO:0005791rough endoplasmic reticulum0.0130046817132735
GO:0044424intracellular part0.0130046817132735
GO:0009066aspartate family amino acid metabolic process0.0202044284172302
GO:0050678regulation of epithelial cell proliferation0.0208221240785165
GO:0043231intracellular membrane-bound organelle0.0208221240785165
GO:0043227membrane-bound organelle0.0208221240785165
GO:0050673epithelial cell proliferation0.0211587578541618
GO:0008283cell proliferation0.0240554820540468
GO:0005622intracellular0.0245856893432835
GO:0001666response to hypoxia0.028377623610498
GO:0019538protein metabolic process0.0322888692633528
GO:0031974membrane-enclosed lumen0.0353706228375008
GO:0043233organelle lumen0.0353706228375008
GO:0043229intracellular organelle0.0420348181285098
GO:0043226organelle0.0420348181285098
GO:0008652amino acid biosynthetic process0.0429255537871426
GO:0048523negative regulation of cellular process0.0433668328287759
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.0433668328287759
GO:0016859cis-trans isomerase activity0.0433668328287759
GO:0048519negative regulation of biological process0.0433668328287759
GO:0043170macromolecule metabolic process0.0433668328287759



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
epithelial vesicle6.18e-2578
vasculature7.89e-2578
vascular system7.89e-2578
epithelial tube2.78e-23117
mesenchyme3.95e-23160
entire embryonic mesenchyme3.95e-23160
splanchnic layer of lateral plate mesoderm7.19e-2383
unilaminar epithelium7.28e-23148
somite1.44e-2271
presomitic mesoderm1.44e-2271
presumptive segmental plate1.44e-2271
dermomyotome1.44e-2271
trunk paraxial mesoderm1.44e-2271
dense mesenchyme tissue2.47e-2273
paraxial mesoderm7.22e-2272
presumptive paraxial mesoderm7.22e-2272
multilaminar epithelium4.10e-2183
skeletal muscle tissue6.28e-2162
striated muscle tissue6.28e-2162
myotome6.28e-2162
trunk mesenchyme9.95e-21122
vessel1.06e-2068
muscle tissue9.60e-2064
musculature9.60e-2064
musculature of body9.60e-2064
epithelial tube open at both ends1.10e-1959
blood vessel1.10e-1959
blood vasculature1.10e-1959
vascular cord1.10e-1959
artery1.84e-1942
arterial blood vessel1.84e-1942
arterial system1.84e-1942
cardiovascular system1.16e-18109
circulatory system1.04e-17112
trunk1.14e-17199
organism subdivision2.12e-17264
cell layer3.39e-16309
epithelium1.21e-15306
systemic artery2.31e-1533
systemic arterial system2.31e-1533
multi-tissue structure2.02e-12342
anatomical cluster7.57e-12373
multi-cellular organism7.58e-12656
anatomical group3.17e-09625
anatomical system3.33e-09624
aorta4.21e-0921
aortic system4.21e-0921
anatomical conduit9.72e-09240
integument2.33e-0846
integumental system2.33e-0846
tube7.95e-08192
skin of body3.06e-0741
surface structure3.11e-0799
Disease
Ontology termp-valuen
ovarian cancer5.21e-0714


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)
MA0003.11.92888
MA0004.10.349539
MA0006.10.210781
MA0007.10.885261
MA0009.10.79061
MA0014.11.06611
MA0017.10.682686
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.637069
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.185335
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.12.24189
MA0056.10
MA0057.12.60171
MA0058.10.265212
MA0059.10.729981
MA0060.10.763267
MA0061.10.330174
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.943943
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.13.00767
MA0074.11.11883
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.730303
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.248289
MA0089.10
MA0090.10.792817
MA0091.10.927876
MA0092.10.318032
MA0093.10.61153
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.11.0054
MA0106.12.10296
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.307853
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.822953
MA0146.11.56298
MA0147.10.946858
MA0148.10.372124
MA0149.10.396509
MA0062.20.320507
MA0035.20.404774
MA0039.22.82436
MA0138.20.534556
MA0002.20.358551
MA0137.20.229531
MA0104.20.760822
MA0047.20.47109
MA0112.20.487949
MA0065.20.839576
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.11.89039
MA0155.11.09568
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.489747
MA0160.10.386031
MA0161.10
MA0162.10.761942
MA0163.12.16871
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.26.40423
MA0102.21.32663
MA0258.10.420151
MA0259.10.504687
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
FOSL1#8061310.83097628628350.002262017389722720.0128441708348421
HEY1#2346282.938262576804150.001105997388051380.00768575828136922
IRF1#365953.471438069801770.008947162075865850.0339337131873971
POLR2A#5430101.952230160507340.00304073181841430.0161350975705401
TAF1#687282.431306389632940.004204244189139110.0200176457200592
TBP#690872.358854073606790.0117973486056640.0429798475957352
ZNF143#770256.13676206919450.0007037131354637180.00565782110505737
ZNF263#1012753.737200744095760.006510908182094970.027878838080842



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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