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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:44, 17 September 2013


Full id: C1401_Smooth_Fibroblast_leiomyoma_malignant_Small_Skeletal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr14:90863344..90863356,+p11@CALM3
p13@CALM1
p9@CALM2
Hg19::chr4:43341736..43341745,+p@chr4:43341736..43341745
+
Hg19::chr4:43341753..43341762,+p@chr4:43341753..43341762
+
Hg19::chr4:43341772..43341787,+p@chr4:43341772..43341787
+
Hg19::chr4:43341791..43341824,+p@chr4:43341791..43341824
+
Hg19::chr4:43341835..43341849,+p@chr4:43341835..43341849
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
somite9.31e-1671
presomitic mesoderm9.31e-1671
presumptive segmental plate9.31e-1671
dermomyotome9.31e-1671
trunk paraxial mesoderm9.31e-1671
paraxial mesoderm2.07e-1572
presumptive paraxial mesoderm2.07e-1572
multilaminar epithelium2.43e-1583
dense mesenchyme tissue4.51e-1573
skeletal muscle tissue6.87e-1462
striated muscle tissue6.87e-1462
myotome6.87e-1462
epithelial vesicle1.61e-1378
muscle tissue3.31e-1364
musculature3.31e-1364
musculature of body3.31e-1364
female organism2.28e-0941
female gonad2.53e-0913
smooth muscle tissue3.60e-0915
trunk mesenchyme7.45e-09122
female reproductive organ2.03e-0837
female reproductive system2.03e-0837
right ovary3.96e-085
left ovary6.24e-084
reproductive structure1.42e-0759
reproductive system1.42e-0759
blood vessel smooth muscle1.79e-0710
arterial system smooth muscle1.79e-0710
artery smooth muscle tissue1.79e-0710
aorta smooth muscle tissue1.79e-0710
adipose tissue1.89e-0714
unilaminar epithelium5.77e-07148
Disease
Ontology termp-valuen
ovarian cancer1.34e-1514
female reproductive organ cancer2.99e-0927
reproductive organ cancer2.27e-0829
benign neoplasm5.51e-084
cell type benign neoplasm9.24e-073
leiomyoma9.24e-073


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.15.0451
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.12.88836
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.11.61362
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.10.232472
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.22.67639
MA0035.20.621793
MA0039.20.0313803
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.12.81343
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.347838
MA0163.10.0270301
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.22.58359
MA0079.20.00575781
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
EP300#203366.77394172622321.03454107484288e-050.00026944248208358
FOS#235357.498296090745349.22669120642035e-050.00134322052259177
STAT3#677458.766220830961874.28672496720299e-050.000766218156511574



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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