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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.604211173178243,0

Latest revision as of 11:29, 17 September 2013


Full id: C706_Adipocyte_Preadipocyte_tenocyte_leiomyoma_chorionic_Olfactory_Hair



Phase1 CAGE Peaks

Hg19::chr17:76850062..76850090,-p@chr17:76850062..76850090
-
Hg19::chr17:76850123..76850137,-p@chr17:76850123..76850137
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Hg19::chr17:76850216..76850253,-p8@TIMP2
Hg19::chr17:76850381..76850397,-p3@TIMP2
Hg19::chr17:76850613..76850641,-p5@TIMP2
Hg19::chr17:76850688..76850705,-p9@TIMP2
Hg19::chr17:76851239..76851259,-p4@TIMP2
Hg19::chr17:76851266..76851308,-p6@TIMP2
Hg19::chr17:76851469..76851493,-p@chr17:76851469..76851493
-
Hg19::chr17:76851547..76851576,-p@chr17:76851547..76851576
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Hg19::chr17:76851684..76851703,-p@chr17:76851684..76851703
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Hg19::chr17:76853697..76853720,-p@chr17:76853697..76853720
-


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>

Uber Anatomy
Ontology termp-valuen
multi-cellular organism3.41e-14656
mesoderm7.12e-13315
mesoderm-derived structure7.12e-13315
presumptive mesoderm7.12e-13315
anatomical system2.55e-12624
anatomical group3.70e-12625
epithelial vesicle2.52e-1178
dense mesenchyme tissue7.38e-1173
paraxial mesoderm1.76e-1072
presumptive paraxial mesoderm1.76e-1072
somite2.23e-1071
presomitic mesoderm2.23e-1071
presumptive segmental plate2.23e-1071
dermomyotome2.23e-1071
trunk paraxial mesoderm2.23e-1071
trunk mesenchyme2.54e-10122
muscle tissue9.61e-1064
musculature9.61e-1064
musculature of body9.61e-1064
skeletal muscle tissue1.39e-0962
striated muscle tissue1.39e-0962
myotome1.39e-0962
mesenchyme2.32e-09160
entire embryonic mesenchyme2.32e-09160
vasculature3.45e-0878
vascular system3.45e-0878
splanchnic layer of lateral plate mesoderm7.64e-0883
multilaminar epithelium1.58e-0783
germ layer1.88e-07560
germ layer / neural crest1.88e-07560
embryonic tissue1.88e-07560
presumptive structure1.88e-07560
germ layer / neural crest derived structure1.88e-07560
epiblast (generic)1.88e-07560
vessel3.99e-0768
embryonic structure4.55e-07564
integument6.95e-0746
integumental system6.95e-0746
organ7.22e-07503


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)
MA0003.10.00869098
MA0004.10.32225
MA0006.11.66321
MA0007.10.825205
MA0009.10.756202
MA0014.10.0339142
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.12.48999
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.11.00007
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.00698536
MA0056.10
MA0057.10.3421
MA0058.10.240796
MA0059.10.239727
MA0060.10.103131
MA0061.10.605357
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.11.83363e-05
MA0074.11.05467
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.20556
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.793019
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.11.02503
MA0105.10.130274
MA0106.10.452066
MA0107.10.427483
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.11.34132
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.11.20117
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.0781324
MA0140.12.62247
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.13.22091
MA0145.10.0212759
MA0146.10.139505
MA0147.10.865676
MA0148.10.910784
MA0149.10.367947
MA0062.20.0823902
MA0035.20.981089
MA0039.20.0117227
MA0138.20.503176
MA0002.20.652621
MA0137.21.1244
MA0104.20.335786
MA0047.21.96345
MA0112.20.416057
MA0065.20.452385
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.30107
MA0155.11.75094
MA0156.10.208455
MA0157.12.30745
MA0158.10
MA0159.10.441451
MA0160.10.357736
MA0161.10
MA0162.10.0188054
MA0163.10.0369192
MA0164.11.20414
MA0080.20.558855
MA0018.21.14938
MA0099.20.382887
MA0079.20.00267243
MA0102.21.28978
MA0258.11.23455
MA0259.10.455773
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
GATA2#262444.248310577851330.01122661586864120.0412212253798697
TAL1#688649.956205559146730.0005005618117785480.00441203266607644



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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