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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.665915502040858

Latest revision as of 11:34, 17 September 2013


Full id: C962_Renal_Endothelial_Preadipocyte_Adipocyte_Hepatic_chorionic_tenocyte



Phase1 CAGE Peaks

Hg19::chr9:130580482..130580516,-p@chr9:130580482..130580516
-
Hg19::chr9:130582222..130582259,-p@chr9:130582222..130582259
-
Hg19::chr9:130586651..130586690,+p@chr9:130586651..130586690
+
Hg19::chr9:130587552..130587570,-p11@ENG
Hg19::chr9:130587571..130587595,-p8@ENG
Hg19::chr9:130588024..130588035,-p12@ENG
Hg19::chr9:130588904..130588928,-p@chr9:130588904..130588928
-
Hg19::chr9:130605421..130605442,-p@chr9:130605421..130605442
-
Hg19::chr9:130605459..130605479,-p@chr9:130605459..130605479
-


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
mesoderm9.90e-26315
mesoderm-derived structure9.90e-26315
presumptive mesoderm9.90e-26315
vessel6.53e-2568
splanchnic layer of lateral plate mesoderm1.79e-2483
vasculature3.75e-2378
vascular system3.75e-2378
epithelial tube open at both ends3.95e-2159
blood vessel3.95e-2159
blood vasculature3.95e-2159
vascular cord3.95e-2159
circulatory system4.60e-20112
cardiovascular system5.62e-19109
lateral plate mesoderm1.09e-17203
artery4.58e-1542
arterial blood vessel4.58e-1542
arterial system4.58e-1542
epithelial tube8.15e-15117
systemic artery3.30e-1233
systemic arterial system3.30e-1233
blood vessel endothelium8.18e-1218
endothelium8.18e-1218
cardiovascular system endothelium8.18e-1218
musculoskeletal system1.24e-11167
epithelial vesicle7.95e-1178
unilaminar epithelium1.50e-10148
dense mesenchyme tissue3.15e-1073
somite4.58e-1071
presomitic mesoderm4.58e-1071
presumptive segmental plate4.58e-1071
dermomyotome4.58e-1071
trunk paraxial mesoderm4.58e-1071
paraxial mesoderm5.15e-1072
presumptive paraxial mesoderm5.15e-1072
squamous epithelium7.72e-1025
multi-cellular organism1.08e-09656
simple squamous epithelium1.84e-0922
anatomical system4.98e-09624
anatomical group7.08e-09625
muscle tissue9.77e-0964
musculature9.77e-0964
musculature of body9.77e-0964
primary circulatory organ1.04e-0827
skeletal muscle tissue1.16e-0862
striated muscle tissue1.16e-0862
myotome1.16e-0862
trunk mesenchyme8.60e-08122
aorta9.78e-0821
aortic system9.78e-0821
heart1.22e-0724
primitive heart tube1.22e-0724
primary heart field1.22e-0724
anterior lateral plate mesoderm1.22e-0724
heart tube1.22e-0724
heart primordium1.22e-0724
cardiac mesoderm1.22e-0724
cardiogenic plate1.22e-0724
heart rudiment1.22e-0724
multilaminar epithelium2.14e-0783
tissue2.20e-07773
connective tissue3.56e-07371
endothelial tube5.27e-079
arterial system endothelium5.27e-079
endothelium of artery5.27e-079


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)
MA0003.10.169975
MA0004.11.06719
MA0006.10.733408
MA0007.10.397529
MA0009.10.870971
MA0014.10.0956087
MA0017.10.815464
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.11.40203
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.11.41801
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.22215
MA0056.10
MA0057.10.539841
MA0058.11.56347
MA0059.12.3679
MA0060.10.488252
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.354973
MA0069.10.856287
MA0070.10.845142
MA0071.11.20007
MA0072.10.840664
MA0073.10.447621
MA0074.11.27017
MA0076.10.339975
MA0077.10.832987
MA0078.11.47707
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.11.01254
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.11.35827
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.11.31682
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.582067
MA0115.11.11137
MA0116.14.17597
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.808973
MA0140.10.474342
MA0141.15.27275
MA0142.10.679161
MA0143.10.571113
MA0144.10.552298
MA0145.10.177438
MA0146.11.73307
MA0147.11.14329
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.323611
MA0138.20.608783
MA0002.21.45266
MA0137.20.28622
MA0104.20.943754
MA0047.20.542971
MA0112.22.52701
MA0065.20.719797
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.842081
MA0155.10.645215
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.11.14546
MA0160.12.98265
MA0161.10
MA0162.10.14518
MA0163.11.94603
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.0240304
MA0102.21.41188
MA0258.14.75366
MA0259.10.218904
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#14069036.582158119658120.008659511962914930.0329624510658918



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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