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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=1.08493942895498,

Latest revision as of 12:00, 17 September 2013


Full id: C2179_Preadipocyte_myeloma_Fibroblast_Adipocyte_Multipotent_neurofibroma_Olfactory



Phase1 CAGE Peaks

Hg19::chr12:105478218..105478244,-p1@ALDH1L2
Hg19::chr12:105478259..105478266,-p4@ALDH1L2
Hg19::chr12:105478305..105478329,-p3@ALDH1L2
Hg19::chr12:105478339..105478361,-p2@ALDH1L2


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
dense mesenchyme tissue2.89e-1673
somite6.20e-1671
presomitic mesoderm6.20e-1671
presumptive segmental plate6.20e-1671
dermomyotome6.20e-1671
trunk paraxial mesoderm6.20e-1671
paraxial mesoderm8.26e-1672
presumptive paraxial mesoderm8.26e-1672
multilaminar epithelium1.69e-1483
skeletal muscle tissue7.30e-1462
striated muscle tissue7.30e-1462
myotome7.30e-1462
muscle tissue1.47e-1364
musculature1.47e-1364
musculature of body1.47e-1364
surface structure5.95e-1399
epithelial vesicle2.19e-1278
multi-cellular organism6.50e-10656
organism subdivision7.95e-10264
integument1.50e-0946
integumental system1.50e-0946
skin of body1.86e-0841
trunk4.76e-08199
mesenchyme1.44e-07160
entire embryonic mesenchyme1.44e-07160
trunk mesenchyme2.42e-07122
anatomical system4.87e-07624
anatomical group7.90e-07625
multi-tissue structure8.86e-07342


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)
MA0003.12.39007
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.12.70386
MA0014.13.08565
MA0017.10.577281
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.14.77747
MA0089.10
MA0090.10.640115
MA0091.11.70187
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.13.36866
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.12.00595
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
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
MA0139.16.60408
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.92815
MA0145.13.19603
MA0146.117.2765
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.216.7925
MA0138.26.62981
MA0002.21.75253
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.24.85059
MA0065.20.199162
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
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.35343
MA0102.21.75932
MA0258.11.88931
MA0259.10.471671
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
CCNT2#90546.336201576962630.0006203100587215640.00511403238260352
E2F1#186944.907389214879320.001724022357361790.0106289947450123
E2F6#187645.017155731697390.00157802193473060.00995331760123982
HEY1#2346244.040111043105710.00375304636917980.0185615575011019
MYC#460945.22228187160940.001344309395272740.00885961563279418
SIN3A#2594245.408884726815140.001168172384885160.00794547415858162
TAF1#687243.343046285745290.008005664898701650.0321343493737462
TBP#690843.706770687096390.005296377814784350.0243559685878324



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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