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Coexpression cluster:C1219: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1219_Smooth_Tracheal_penis_tongue_skeletal_leiomyoma_diaphragm
|id=C1219
}}

Latest revision as of 11:40, 17 September 2013


Full id: C1219_Smooth_Tracheal_penis_tongue_skeletal_leiomyoma_diaphragm



Phase1 CAGE Peaks

Hg19::chr16:30078811..30078840,+p12@ALDOA
Hg19::chr16:30078876..30078906,+p9@ALDOA
Hg19::chr16:30079963..30079982,+p17@ALDOA
Hg19::chr16:30080136..30080158,+p15@ALDOA
Hg19::chr16:30080170..30080194,+p16@ALDOA
Hg19::chr16:30080217..30080237,+p14@ALDOA
Hg19::chr16:30080645..30080685,+p@chr16:30080645..30080685
+


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
epithelial vesicle8.98e-1678
dense mesenchyme tissue1.46e-1473
paraxial mesoderm2.30e-1472
presumptive paraxial mesoderm2.30e-1472
somite3.42e-1471
presomitic mesoderm3.42e-1471
presumptive segmental plate3.42e-1471
dermomyotome3.42e-1471
trunk paraxial mesoderm3.42e-1471
artery8.81e-1442
arterial blood vessel8.81e-1442
arterial system8.81e-1442
mesoderm2.54e-13315
mesoderm-derived structure2.54e-13315
presumptive mesoderm2.54e-13315
skeletal muscle tissue1.34e-1262
striated muscle tissue1.34e-1262
myotome1.34e-1262
multilaminar epithelium2.43e-1283
muscle tissue5.15e-1264
musculature5.15e-1264
musculature of body5.15e-1264
epithelial tube open at both ends7.48e-1159
blood vessel7.48e-1159
blood vasculature7.48e-1159
vascular cord7.48e-1159
systemic artery3.38e-1033
systemic arterial system3.38e-1033
splanchnic layer of lateral plate mesoderm3.94e-1083
musculoskeletal system1.02e-09167
vessel1.26e-0968
vasculature9.50e-0978
vascular system9.50e-0978
lateral plate mesoderm3.44e-08203
trunk mesenchyme4.51e-08122
circulatory system1.33e-07112
cardiovascular system5.26e-07109
epithelial tube8.23e-07117


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)
MA0003.10.0137961
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.187674
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.11.4376
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.11.04442
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.00958848
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.13.13765
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.12.96741
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.78583
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.11.83545
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.581146
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.563664
MA0035.20.564239
MA0039.21.14159
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.21.95102
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.910701
MA0156.12.57306
MA0157.10.749547
MA0158.10
MA0159.11.40717
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.632664
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.07638
MA0102.21.51913
MA0258.11.97124
MA0259.10.289405
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
CTCF#1066464.594505462635740.0002478392075687640.00267508050839956
POLR2A#543072.147453176558070.004747636447610280.022342108004865
RAD21#588545.917162225975040.002393184937227960.01355432980798
SMC3#912648.597104482818770.0005798466280161370.00486727230215217



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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