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Coexpression cluster:C2219: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2219_Smooth_Mesenchymal_Pericytes_mesenchymal_Melanocyte_Preadipocyte_Monocytederived
|id=C2219
}}

Latest revision as of 12:01, 17 September 2013


Full id: C2219_Smooth_Mesenchymal_Pericytes_mesenchymal_Melanocyte_Preadipocyte_Monocytederived



Phase1 CAGE Peaks

Hg19::chr12:56122186..56122205,-p7@CD63
Hg19::chr12:56122207..56122218,-p16@CD63
Hg19::chr12:56122220..56122248,-p4@CD63
Hg19::chr12:56122781..56122804,-p1@CD63


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 vesicle7.52e-2478
somite1.13e-2271
presomitic mesoderm1.13e-2271
presumptive segmental plate1.13e-2271
dermomyotome1.13e-2271
trunk paraxial mesoderm1.13e-2271
dense mesenchyme tissue6.01e-2273
paraxial mesoderm7.33e-2272
presumptive paraxial mesoderm7.33e-2272
multilaminar epithelium8.87e-2283
musculoskeletal system1.71e-21167
mesoderm3.66e-21315
mesoderm-derived structure3.66e-21315
presumptive mesoderm3.66e-21315
skeletal muscle tissue1.96e-2062
striated muscle tissue1.96e-2062
myotome1.96e-2062
muscle tissue2.74e-1964
musculature2.74e-1964
musculature of body2.74e-1964
trunk mesenchyme1.06e-17122
unilaminar epithelium2.64e-16148
vasculature3.42e-1678
vascular system3.42e-1678
mesenchyme4.03e-16160
entire embryonic mesenchyme4.03e-16160
trunk4.47e-16199
artery3.86e-1542
arterial blood vessel3.86e-1542
arterial system3.86e-1542
organism subdivision1.57e-14264
epithelial tube3.13e-14117
splanchnic layer of lateral plate mesoderm1.04e-1383
vessel3.43e-1368
epithelial tube open at both ends9.30e-1359
blood vessel9.30e-1359
blood vasculature9.30e-1359
vascular cord9.30e-1359
systemic artery1.45e-1233
systemic arterial system1.45e-1233
multi-cellular organism7.73e-12656
anatomical system1.06e-11624
anatomical group1.97e-11625
cardiovascular system2.04e-09109
circulatory system4.04e-09112
lateral plate mesoderm4.91e-09203
Disease
Ontology termp-valuen
ovarian cancer2.56e-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)
MA0003.14.10305
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.12.32784
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
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.11.47051
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
MA0073.18.301
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
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
MA0145.11.08195
MA0146.12.92476
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.27.89088
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.22.35508
MA0065.23.22574
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.12.30186
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.13.14178
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.212.5948
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
ELF1#199744.258097958807540.003041525565781240.0160642201155369
EP300#203346.77394172622320.0004748459821442640.00433576145560105
TCF7L2#693438.077632422353010.002978381685834620.0158598483091257
YY1#752844.911170749853860.00171871838055440.0106661850939878
ZBTB7A#5134147.35190930787590.000342223540015990.00346063945543474



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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