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Coexpression cluster:C2831: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2831_Smooth_Fibroblast_cholangiocellular_osteoclastoma_basal_spindle_Ewing
|id=C2831
}}

Latest revision as of 12:13, 17 September 2013


Full id: C2831_Smooth_Fibroblast_cholangiocellular_osteoclastoma_basal_spindle_Ewing



Phase1 CAGE Peaks

Hg19::chr5:83680192..83680209,-p5@EDIL3
Hg19::chr5:83680211..83680254,-p3@EDIL3
Hg19::chr5:83680261..83680270,-p10@EDIL3
Hg19::chr5:83680271..83680298,-p6@EDIL3


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
anatomical cluster2.01e-18373
multi-tissue structure7.14e-18342
multi-cellular organism3.76e-15656
skeletal muscle tissue1.64e-1262
striated muscle tissue1.64e-1262
myotome1.64e-1262
muscle tissue2.52e-1264
musculature2.52e-1264
musculature of body2.52e-1264
structure with developmental contribution from neural crest8.89e-12132
tube9.11e-12192
dense mesenchyme tissue1.86e-1173
anatomical system4.17e-11624
paraxial mesoderm4.27e-1172
presumptive paraxial mesoderm4.27e-1172
artery4.37e-1142
arterial blood vessel4.37e-1142
arterial system4.37e-1142
anatomical group5.32e-11625
somite5.62e-1171
presomitic mesoderm5.62e-1171
presumptive segmental plate5.62e-1171
dermomyotome5.62e-1171
trunk paraxial mesoderm5.62e-1171
splanchnic layer of lateral plate mesoderm8.26e-1183
epithelial vesicle1.98e-1078
anatomical conduit2.06e-10240
cell layer2.27e-10309
mesenchyme2.46e-10160
entire embryonic mesenchyme2.46e-10160
epithelium5.11e-10306
systemic artery6.39e-1033
systemic arterial system6.39e-1033
epithelial tube1.14e-09117
vasculature3.48e-0978
vascular system3.48e-0978
central nervous system1.24e-0881
epithelial tube open at both ends1.43e-0859
blood vessel1.43e-0859
blood vasculature1.43e-0859
vascular cord1.43e-0859
nervous system1.66e-0889
ectoderm-derived structure2.65e-08171
ectoderm2.65e-08171
presumptive ectoderm2.65e-08171
embryo4.00e-08592
trunk mesenchyme5.30e-08122
cardiovascular system6.63e-08109
circulatory system8.98e-08112
multilaminar epithelium9.46e-0883
organism subdivision1.50e-07264
developing anatomical structure2.98e-07581
brain3.26e-0768
future brain3.26e-0768
heart6.71e-0724
primitive heart tube6.71e-0724
primary heart field6.71e-0724
anterior lateral plate mesoderm6.71e-0724
heart tube6.71e-0724
heart primordium6.71e-0724
cardiac mesoderm6.71e-0724
cardiogenic plate6.71e-0724
heart rudiment6.71e-0724
neural plate9.67e-0782
presumptive neural plate9.67e-0782
embryonic structure9.81e-07564


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)
MA0003.13.49532
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.22.35508
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
TAF1#687243.343046285745290.008005664898701650.0323181800608984



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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