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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.698847673570409,0

Latest revision as of 11:21, 17 September 2013


Full id: C384_Adipocyte_smooth_bladder_left_aorta_Osteoblast_colon



Phase1 CAGE Peaks

Hg19::chr11:117075220..117075249,+p1@uc001pqq.1
Hg19::chr1:201869414..201869432,+p@chr1:201869414..201869432
+
Hg19::chr20:35173246..35173275,+p3@MYL9
Hg19::chr20:35173334..35173350,+p6@MYL9
Hg19::chr20:35173392..35173405,+p8@MYL9
Hg19::chr20:35173425..35173448,+p4@MYL9
Hg19::chr20:35176429..35176448,+p@chr20:35176429..35176448
+
Hg19::chr20:35176459..35176471,+p@chr20:35176459..35176471
+
Hg19::chr20:35176468..35176476,-p@chr20:35176468..35176476
-
Hg19::chr20:35176474..35176493,+p@chr20:35176474..35176493
+
Hg19::chr20:35176518..35176542,+p@chr20:35176518..35176542
+
Hg19::chr20:35176544..35176572,+p@chr20:35176544..35176572
+
Hg19::chr20:35177479..35177514,+p@chr20:35177479..35177514
+
Hg19::chr20:35177539..35177547,+p@chr20:35177539..35177547
+
Hg19::chr20:35177588..35177615,-p@chr20:35177588..35177615
-
Hg19::chr20:35177596..35177615,+p@chr20:35177596..35177615
+
Hg19::chr20:35177635..35177755,-p@chr20:35177635..35177755
-
Hg19::chr20:35177642..35177704,+p@chr20:35177642..35177704
+
Hg19::chr20:35177709..35177724,+p@chr20:35177709..35177724
+
Hg19::chr20:35177756..35177772,+p@chr20:35177756..35177772
+
Hg19::chr20:35177820..35177829,+p@chr20:35177820..35177829
+
Hg19::chr20:35177847..35177864,+p@chr20:35177847..35177864
+
Hg19::chr20:35177969..35177986,+p@chr20:35177969..35177986
+
Hg19::chr20:35178012..35178028,+p@chr20:35178012..35178028
+
Hg19::chr20:35178034..35178046,+p@chr20:35178034..35178046
+
Hg19::chr20:35178050..35178086,-p@chr20:35178050..35178086
-
Hg19::chr20:35178057..35178112,+p@chr20:35178057..35178112
+
Hg19::chr20:35178101..35178139,-p@chr20:35178101..35178139
-


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:0005859muscle myosin complex0.0105086541858001
GO:0016460myosin II complex0.0105086541858001
GO:0006937regulation of muscle contraction0.0105086541858001
GO:0008307structural constituent of muscle0.0105086541858001
GO:0044449contractile fiber part0.0106754582204953
GO:0043292contractile fiber0.0106754582204953
GO:0016459myosin complex0.0152983128963348
GO:0003012muscle system process0.0183484438164763
GO:0006936muscle contraction0.0183484438164763
GO:0051239regulation of multicellular organismal process0.0269312696017041
GO:0015629actin cytoskeleton0.0269312696017041



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
mesenchyme2.85e-16160
entire embryonic mesenchyme2.85e-16160
trunk mesenchyme6.69e-15122
muscle tissue2.33e-1464
musculature2.33e-1464
musculature of body2.33e-1464
epithelial vesicle9.75e-1478
dense mesenchyme tissue1.14e-1373
skeletal muscle tissue2.64e-1362
striated muscle tissue2.64e-1362
myotome2.64e-1362
paraxial mesoderm4.00e-1372
presumptive paraxial mesoderm4.00e-1372
somite4.10e-1371
presomitic mesoderm4.10e-1371
presumptive segmental plate4.10e-1371
dermomyotome4.10e-1371
trunk paraxial mesoderm4.10e-1371
multilaminar epithelium1.23e-1083
trunk1.06e-09199
mesoderm1.45e-09315
mesoderm-derived structure1.45e-09315
presumptive mesoderm1.45e-09315
organism subdivision3.85e-09264
multi-tissue structure1.76e-08342
splanchnic layer of lateral plate mesoderm8.30e-0883
primary circulatory organ3.42e-0727
artery5.62e-0742
arterial blood vessel5.62e-0742
arterial system5.62e-0742
intermediate mesoderm6.12e-0728
systemic artery6.55e-0733
systemic arterial system6.55e-0733
adipose tissue6.83e-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)
MA0003.10.33535
MA0004.13.01913
MA0006.10.641722
MA0007.11.11011
MA0009.10.441048
MA0014.10.00912243
MA0017.12.76234
MA0019.10.197704
MA0024.10.354374
MA0025.10.557187
MA0027.11.98963
MA0028.10.0452766
MA0029.10.369985
MA0030.10.360703
MA0031.10.309631
MA0038.10.168286
MA0040.10.374747
MA0041.10.11856
MA0042.10.10161
MA0043.10.441316
MA0046.10.431829
MA0048.10.466262
MA0050.10.102063
MA0051.10.165625
MA0052.10.377904
MA0055.10.12662
MA0056.10
MA0057.10.160938
MA0058.10.22757
MA0059.10.844514
MA0060.10.0117157
MA0061.17.26479
MA0063.10
MA0066.10.168556
MA0067.10.724802
MA0068.15.08324
MA0069.10.428576
MA0070.10.419162
MA0071.10.144505
MA0072.10.415392
MA0073.114.6899
MA0074.10.165153
MA0076.10.0703269
MA0077.10.408948
MA0078.10.232083
MA0081.10.490371
MA0083.10.447432
MA0084.10.901266
MA0087.10.413345
MA0088.10.650889
MA0089.10
MA0090.10.264964
MA0091.12.35449
MA0092.10.629894
MA0093.13.68209
MA0095.10
MA0098.10
MA0100.10.17714
MA0101.14.39102
MA0103.10.146349
MA0105.14.59522
MA0106.12.40696
MA0107.12.38616
MA0108.20.307261
MA0109.10
MA0111.10.282297
MA0113.10.206168
MA0114.10.428308
MA0115.10.654355
MA0116.10.0221565
MA0117.10.473208
MA0119.10.0566716
MA0122.10.495633
MA0124.10.616574
MA0125.10.541304
MA0130.10
MA0131.10.245067
MA0132.10
MA0133.10
MA0135.10.466979
MA0136.10.172767
MA0139.10.00650158
MA0140.10.865299
MA0141.10.486202
MA0142.10.285297
MA0143.10.206288
MA0144.10.0172203
MA0145.11.23853
MA0146.10.122035
MA0147.10.0229785
MA0148.10.122067
MA0149.10.137231
MA0062.20.232741
MA0035.20.142505
MA0039.20.334674
MA0138.20.232954
MA0002.23.78849
MA0137.20.0475444
MA0104.20.0565825
MA0047.20.187056
MA0112.20.91029
MA0065.20.566955
MA0150.10.0740738
MA0151.10
MA0152.10.146841
MA0153.10.526421
MA0154.10.127455
MA0155.14.37891
MA0156.10.0483557
MA0157.10.264816
MA0158.10
MA0159.11.95683
MA0160.10.130642
MA0161.10
MA0162.10.00142521
MA0163.10.0752725
MA0164.10.214689
MA0080.21.44118
MA0018.20.196028
MA0099.20.147056
MA0079.22.91436
MA0102.20.936833
MA0258.13.13387
MA0259.11.55388
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
CTCFL#14069064.231387362637360.002416712809055170.0136196346354907
SPI1#6688113.223127092633930.000256585273209660.00276149107056303



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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