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Coexpression cluster:C471: Difference between revisions

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{{Coexpression_clusters
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|full_id=C471_Smooth_Fibroblast_leiomyoma_mesenchymal_Mesothelial_meningioma_Prostate
|id=C471
}}

Latest revision as of 11:23, 17 September 2013


Full id: C471_Smooth_Fibroblast_leiomyoma_mesenchymal_Mesothelial_meningioma_Prostate



Phase1 CAGE Peaks

Hg19::chr8:42033234..42033247,-p@chr8:42033234..42033247
-
Hg19::chr8:42033253..42033264,-p@chr8:42033253..42033264
-
Hg19::chr8:42033364..42033376,-p@chr8:42033364..42033376
-
Hg19::chr8:42033383..42033398,-p@chr8:42033383..42033398
-
Hg19::chr8:42033546..42033576,-p@chr8:42033546..42033576
-
Hg19::chr8:42033578..42033605,-p@chr8:42033578..42033605
-
Hg19::chr8:42033607..42033639,-p@chr8:42033607..42033639
-
Hg19::chr8:42033640..42033671,-p@chr8:42033640..42033671
-
Hg19::chr8:42036444..42036460,+p@chr8:42036444..42036460
+
Hg19::chr8:42036539..42036561,-p@chr8:42036539..42036561
-
Hg19::chr8:42037500..42037536,-p@chr8:42037500..42037536
-
Hg19::chr8:42037883..42037900,-p@chr8:42037883..42037900
-
Hg19::chr8:42038055..42038068,-p3@PLAT
Hg19::chr8:42040287..42040298,-p10@PLAT
Hg19::chr8:42042635..42042650,-p4@PLAT
Hg19::chr8:42042654..42042665,-p9@PLAT
Hg19::chr8:42044953..42044969,-p@chr8:42044953..42044969
-
Hg19::chr8:42044977..42044996,-p@chr8:42044977..42044996
-
Hg19::chr8:42045498..42045512,-p6@PLAT
Hg19::chr8:42065075..42065090,-p1@PLAT
Hg19::chr8:42065187..42065201,-p2@PLAT


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
epithelial vesicle2.04e-2278
skeletal muscle tissue2.67e-2262
striated muscle tissue2.67e-2262
myotome2.67e-2262
muscle tissue3.24e-2264
musculature3.24e-2264
musculature of body3.24e-2264
systemic artery3.51e-2133
systemic arterial system3.51e-2133
somite1.04e-2071
presomitic mesoderm1.04e-2071
presumptive segmental plate1.04e-2071
dermomyotome1.04e-2071
trunk paraxial mesoderm1.04e-2071
artery1.90e-2042
arterial blood vessel1.90e-2042
arterial system1.90e-2042
paraxial mesoderm3.25e-2072
presumptive paraxial mesoderm3.25e-2072
dense mesenchyme tissue9.77e-2073
trunk mesenchyme2.15e-17122
multilaminar epithelium1.35e-1683
epithelial tube1.28e-15117
organism subdivision2.36e-15264
trunk7.74e-15199
smooth muscle tissue1.60e-1415
vasculature2.29e-1478
vascular system2.29e-1478
mesenchyme3.15e-14160
entire embryonic mesenchyme3.15e-14160
epithelial tube open at both ends1.71e-1359
blood vessel1.71e-1359
blood vasculature1.71e-1359
vascular cord1.71e-1359
unilaminar epithelium2.31e-13148
splanchnic layer of lateral plate mesoderm3.42e-1383
cell layer3.76e-13309
epithelium4.08e-13306
blood vessel smooth muscle3.08e-1210
arterial system smooth muscle3.08e-1210
artery smooth muscle tissue3.08e-1210
aorta smooth muscle tissue3.08e-1210
cardiovascular system7.71e-12109
multi-tissue structure1.63e-11342
vessel2.59e-1168
circulatory system3.75e-11112
aorta5.07e-1121
aortic system5.07e-1121
mesoderm4.04e-10315
mesoderm-derived structure4.04e-10315
presumptive mesoderm4.04e-10315
developing anatomical structure4.39e-08581
anatomical system1.12e-07624
embryo1.23e-07592
anatomical group1.33e-07625
anatomical cluster2.39e-07373
excretory tube3.70e-0716
kidney epithelium3.70e-0716
cortex of kidney3.89e-0712
renal parenchyma3.89e-0712
nephron tubule epithelium4.97e-0710
heart blood vessel5.95e-075
coronary vessel5.95e-075
anatomical conduit7.34e-07240
Disease
Ontology termp-valuen
ovarian cancer5.71e-0914


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)
MA0003.10.00063637
MA0004.11.55083
MA0006.10.264032
MA0007.10.156885
MA0009.11.34126
MA0014.10.00441763
MA0017.10.0964051
MA0019.10.757112
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.10.0843345
MA0029.10.467171
MA0030.10.457153
MA0031.10.401568
MA0038.10.24162
MA0040.10.472301
MA0041.10.181587
MA0042.10.160318
MA0043.10.543454
MA0046.10.533373
MA0048.10.591444
MA0050.10.940798
MA0051.11.2467
MA0052.10.475699
MA0055.10.232397
MA0056.10
MA0057.10.0306551
MA0058.11.73668
MA0059.12.35007
MA0060.10.0296044
MA0061.13.52176
MA0063.10
MA0066.10.241938
MA0067.10.83875
MA0068.10.0636439
MA0069.10.529912
MA0070.10.519883
MA0071.10.611515
MA0072.10.515863
MA0073.10.0111205
MA0074.10.23792
MA0076.10.119431
MA0077.10.508982
MA0078.10.846104
MA0081.10.109654
MA0083.10.549943
MA0084.11.01907
MA0087.10.513678
MA0088.10.0105133
MA0089.10
MA0090.10.402075
MA0091.10.170864
MA0092.10.146372
MA0093.11.97611
MA0095.10
MA0098.10
MA0100.10.252028
MA0101.10.971222
MA0103.10.536497
MA0105.15.72317
MA0106.10.272934
MA0107.11.09072
MA0108.21.03141
MA0109.10
MA0111.10.423052
MA0113.10.285689
MA0114.10.68981
MA0115.11.80705
MA0116.11.5622
MA0117.10.577217
MA0119.13.6282
MA0122.10.600851
MA0124.10.727093
MA0125.10.648747
MA0130.10
MA0131.10.329895
MA0132.10
MA0133.10
MA0135.10.570637
MA0136.10.246897
MA0139.10.0845536
MA0140.10.211376
MA0141.10.108582
MA0142.10.374765
MA0143.10.285827
MA0144.11.42189
MA0145.10.211895
MA0146.10.564984
MA0147.11.12418
MA0148.10.546085
MA0149.10.204488
MA0062.20.0205944
MA0035.20.210872
MA0039.27.90025e-05
MA0138.20.848318
MA0002.20.499059
MA0137.21.52875
MA0104.20.850224
MA0047.20.263601
MA0112.20.0983575
MA0065.20.368601
MA0150.10.124469
MA0151.10
MA0152.10.618168
MA0153.10.633172
MA0154.10.484177
MA0155.11.2055
MA0156.10.0888107
MA0157.11.65846
MA0158.10
MA0159.10.187008
MA0160.10.196462
MA0161.10
MA0162.10.000733895
MA0163.10.066224
MA0164.10.801488
MA0080.20.566769
MA0018.20.274004
MA0099.20.216352
MA0079.21.59349e-07
MA0102.21.05522
MA0258.10.608204
MA0259.10.761407
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
MEF2C#420835.901622070374860.01360717439201470.048017289036614



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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