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Coexpression cluster:C4429: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4429_Adipocyte_Preadipocyte_neuroblastoma_Smooth_Fibroblast_Mesenchymal_mesenchymal
|id=C4429
}}

Latest revision as of 12:45, 17 September 2013


Full id: C4429_Adipocyte_Preadipocyte_neuroblastoma_Smooth_Fibroblast_Mesenchymal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr4:80993800..80993850,-p5@ANTXR2
Hg19::chr4:80993855..80993906,-p3@ANTXR2
Hg19::chr4:80993925..80993962,-p4@ANTXR2


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
mesoderm3.21e-22315
mesoderm-derived structure3.21e-22315
presumptive mesoderm3.21e-22315
splanchnic layer of lateral plate mesoderm3.61e-2083
vasculature2.92e-1878
vascular system2.92e-1878
epithelial tube open at both ends3.02e-1859
blood vessel3.02e-1859
blood vasculature3.02e-1859
vascular cord3.02e-1859
vessel4.97e-1868
multi-cellular organism3.87e-16656
cardiovascular system1.36e-15109
circulatory system1.42e-15112
artery1.58e-1542
arterial blood vessel1.58e-1542
arterial system1.58e-1542
anatomical system4.47e-15624
epithelial tube8.14e-15117
anatomical group9.96e-15625
embryonic structure1.43e-13564
unilaminar epithelium2.25e-13148
muscle tissue3.16e-1364
musculature3.16e-1364
musculature of body3.16e-1364
musculoskeletal system6.13e-13167
germ layer6.46e-13560
germ layer / neural crest6.46e-13560
embryonic tissue6.46e-13560
presumptive structure6.46e-13560
germ layer / neural crest derived structure6.46e-13560
epiblast (generic)6.46e-13560
systemic artery8.77e-1333
systemic arterial system8.77e-1333
skeletal muscle tissue1.45e-1262
striated muscle tissue1.45e-1262
myotome1.45e-1262
multilaminar epithelium1.53e-1283
lateral plate mesoderm2.05e-12203
dense mesenchyme tissue3.04e-1273
somite3.57e-1271
presomitic mesoderm3.57e-1271
presumptive segmental plate3.57e-1271
dermomyotome3.57e-1271
trunk paraxial mesoderm3.57e-1271
paraxial mesoderm5.27e-1272
presumptive paraxial mesoderm5.27e-1272
developing anatomical structure1.75e-11581
trunk mesenchyme2.49e-11122
epithelial vesicle2.70e-1178
embryo2.67e-10592
aorta1.92e-0821
aortic system1.92e-0821
tissue4.00e-08773
mesenchyme1.07e-07160
entire embryonic mesenchyme1.07e-07160
blood vessel endothelium7.48e-0718
endothelium7.48e-0718
cardiovascular system endothelium7.48e-0718
Disease
Ontology termp-valuen
ovarian cancer1.77e-0714


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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.13.15032
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.15.08367
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.12.37746
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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#1066435.360256373075030.0064925092527670.0280763187383435
ETS1#211339.728760922202340.001085840092584840.00764281260476262
HMGN3#932438.178547723350590.001827766942164210.0109011565114893
TRIM28#10155212.39368336350830.008368344129438470.0329356908552315
ZNF263#1012738.221841637010680.001799043925565870.010984527830586



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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