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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.571146760034452,0.

Latest revision as of 11:22, 17 September 2013


Full id: C421_Smooth_Fibroblast_epithelioid_hepatic_Sertoli_Ewing_tenocyte



Phase1 CAGE Peaks

Hg19::chr10:74856613..74856631,-p1@P4HA1
Hg19::chr5:121399703..121399718,-p@chr5:121399703..121399718
-
Hg19::chr5:121400446..121400468,-p@chr5:121400446..121400468
-
Hg19::chr5:121400825..121400873,-p@chr5:121400825..121400873
-
Hg19::chr5:121400881..121400901,-p@chr5:121400881..121400901
-
Hg19::chr5:121401627..121401642,-p@chr5:121401627..121401642
-
Hg19::chr5:121401645..121401695,-p@chr5:121401645..121401695
-
Hg19::chr5:121401698..121401726,-p@chr5:121401698..121401726
-
Hg19::chr5:121401731..121401748,-p@chr5:121401731..121401748
-
Hg19::chr5:121401877..121401903,-p@chr5:121401877..121401903
-
Hg19::chr5:121402009..121402030,-p@chr5:121402009..121402030
-
Hg19::chr5:121402258..121402287,-p@chr5:121402258..121402287
-
Hg19::chr5:121406259..121406287,-p@chr5:121406259..121406287
-
Hg19::chr5:121409731..121409737,-p@chr5:121409731..121409737
-
Hg19::chr5:121409743..121409755,-p@chr5:121409743..121409755
-
Hg19::chr5:121411148..121411162,-p@chr5:121411148..121411162
-
Hg19::chr5:121411232..121411247,-p@chr5:121411232..121411247
-
Hg19::chr5:121412666..121412683,-p9@LOX
Hg19::chr5:121413171..121413182,-p5@LOX
Hg19::chr5:121413944..121413965,-p1@LOX
Hg19::chr5:121413974..121413986,-p4@LOX
Hg19::chr5:121414004..121414025,-p3@LOX
Hg19::chr5:121414045..121414063,-p2@LOX
Hg19::chr5:121414152..121414179,-p10@LOX


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:0031545peptidyl-proline 4-dioxygenase activity0.00429753038433406
GO:0048251elastic fiber assembly0.00429753038433406
GO:0004656procollagen-proline 4-dioxygenase activity0.00429753038433406
GO:0019798procollagen-proline dioxygenase activity0.00572961881385015
GO:0031543peptidyl-proline dioxygenase activity0.00572961881385015
GO:0004720protein-lysine 6-oxidase activity0.00572961881385015
GO:0030199collagen fibril organization0.00613869657258434
GO:0031418L-ascorbic acid binding0.01097934462629
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.01097934462629
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.0120286572408851
GO:0016491oxidoreductase activity0.0131707519804101
GO:0030324lung development0.0131707519804101
GO:0030323respiratory tube development0.0131707519804101
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 donors0.0131707519804101
GO:0030198extracellular matrix organization and biogenesis0.0131707519804101
GO:0005581collagen0.014493277316521
GO:0005788endoplasmic reticulum lumen0.0161644116411761
GO:0051213dioxygenase activity0.0171696269856064
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0171696269856064
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0171696269856064
GO:0043062extracellular structure organization and biogenesis0.0171696269856064
GO:0035295tube development0.0218246679385887
GO:0005507copper ion binding0.0218246679385887
GO:0044420extracellular matrix part0.0234131593350398
GO:0001568blood vessel development0.027372249835033
GO:0001944vasculature development0.027372249835033
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0281005465565403
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0321332748221334
GO:0019842vitamin binding0.0361773988863747
GO:0007167enzyme linked receptor protein signaling pathway0.0427874371191506
GO:0046914transition metal ion binding0.0490018528809785



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
dense mesenchyme tissue2.96e-1773
somite4.22e-1771
presomitic mesoderm4.22e-1771
presumptive segmental plate4.22e-1771
dermomyotome4.22e-1771
trunk paraxial mesoderm4.22e-1771
paraxial mesoderm1.30e-1672
presumptive paraxial mesoderm1.30e-1672
skeletal muscle tissue2.02e-1662
striated muscle tissue2.02e-1662
myotome2.02e-1662
muscle tissue2.12e-1564
musculature2.12e-1564
musculature of body2.12e-1564
epithelial vesicle1.18e-1478
multilaminar epithelium1.31e-1483
trunk mesenchyme1.08e-10122
artery1.01e-0942
arterial blood vessel1.01e-0942
arterial system1.01e-0942
systemic artery8.68e-0933
systemic arterial system8.68e-0933
mesenchyme1.02e-08160
entire embryonic mesenchyme1.02e-08160
vasculature1.15e-0878
vascular system1.15e-0878
unilaminar epithelium1.20e-08148
splanchnic layer of lateral plate mesoderm2.72e-0883
cardiovascular system3.09e-08109
integument3.28e-0846
integumental system3.28e-0846
circulatory system1.30e-07112
skin of body1.46e-0741
trunk3.11e-07199
omentum7.79e-076
peritoneum7.79e-076
abdominal cavity7.79e-076
visceral peritoneum7.79e-076
Disease
Ontology termp-valuen
ovarian cancer9.37e-1014


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)
MA0003.11.00557e-06
MA0004.10.13931
MA0006.10.0576274
MA0007.10.128232
MA0009.10.495012
MA0014.10.00150727
MA0017.10.935564
MA0019.10.238234
MA0024.10.404839
MA0025.10.614568
MA0027.12.05626
MA0028.10.0643724
MA0029.11.07975
MA0030.10.41146
MA0031.11.67884
MA0038.10.594428
MA0040.11.09053
MA0041.10.150655
MA0042.11.32287
MA0043.10.495289
MA0046.10.485466
MA0048.10.0201022
MA0050.10.131853
MA0051.10.203156
MA0052.10.429421
MA0055.10.000110579
MA0056.10
MA0057.10.0582452
MA0058.10.086794
MA0059.10.291213
MA0060.10.0198514
MA0061.10.0141489
MA0063.10
MA0066.10.206381
MA0067.10.78548
MA0068.10.247466
MA0069.10.482095
MA0070.10.472333
MA0071.10.531175
MA0072.10.468422
MA0073.17.53709e-06
MA0074.10.202636
MA0076.10.094817
MA0077.10.461731
MA0078.10.275364
MA0081.10.0862369
MA0083.10.501617
MA0084.10.964138
MA0087.10.466297
MA0088.10.0201813
MA0089.10
MA0090.10.102378
MA0091.10.140889
MA0092.10.759879
MA0093.10.0588752
MA0095.10
MA0098.10
MA0100.10.215803
MA0101.10.217713
MA0103.10.0539026
MA0105.10.0469725
MA0106.10.235406
MA0107.10.13479
MA0108.20.355343
MA0109.10
MA0111.10.109681
MA0113.10.247415
MA0114.10.56121
MA0115.10.71383
MA0116.10.0344979
MA0117.10.528241
MA0119.10.569272
MA0122.10.551352
MA0124.11.61864
MA0125.10.598285
MA0130.10
MA0131.10.289284
MA0132.10
MA0133.10
MA0135.10.521813
MA0136.10.606126
MA0139.10.0119363
MA0140.10.178014
MA0141.10.0853004
MA0142.10.88389
MA0143.11.98174
MA0144.10.115718
MA0145.10.390706
MA0146.10.000198722
MA0147.10.141953
MA0148.11.46538
MA0149.10.511388
MA0062.20.0131657
MA0035.20.177548
MA0039.20.000705892
MA0138.20.276299
MA0002.20.20101
MA0137.20.0671912
MA0104.20.0874345
MA0047.22.6301
MA0112.20.022609
MA0065.20.815716
MA0150.10.0992631
MA0151.10
MA0152.10.182375
MA0153.10.583009
MA0154.10.0449168
MA0155.10.329858
MA0156.10.240796
MA0157.12.30125
MA0158.10
MA0159.10.601663
MA0160.10.164277
MA0161.10
MA0162.10.00132146
MA0163.10.01442
MA0164.11.3148
MA0080.20.810379
MA0018.20.236412
MA0099.21.02934
MA0079.22.56124e-05
MA0102.21.00004
MA0258.10.106789
MA0259.10.150791
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
BHLHE40#855359.348294488953630.0001636058871940370.00203511615681968



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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