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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.21899943110996

Latest revision as of 12:15, 17 September 2013


Full id: C2920_liver_Mesenchymal_Neutrophils_Osteoblast_Melanocyte_testis_CD14



Phase1 CAGE Peaks

Hg19::chr8:145065410..145065446,+p7@GRINA
Hg19::chr8:145065457..145065489,+p6@GRINA
Hg19::chr8:145065521..145065547,+p9@GRINA
Hg19::chr8:145065705..145065731,+p5@GRINA


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
multi-cellular organism1.34e-18656
anatomical system7.89e-18624
anatomical group1.85e-17625
germ layer6.48e-16560
germ layer / neural crest6.48e-16560
embryonic tissue6.48e-16560
presumptive structure6.48e-16560
germ layer / neural crest derived structure6.48e-16560
epiblast (generic)6.48e-16560
embryonic structure1.28e-15564
developing anatomical structure1.34e-14581
mesoderm4.65e-14315
mesoderm-derived structure4.65e-14315
presumptive mesoderm4.65e-14315
embryo7.33e-14592
adult organism1.12e-12114
lateral plate mesoderm1.36e-10203
organ2.83e-09503
hemolymphoid system4.97e-09108
immune system1.55e-0893
bone marrow1.76e-0876
hematopoietic system1.90e-0898
blood island1.90e-0898
skeletal system3.85e-08100
skeletal element5.98e-0890
musculoskeletal system6.04e-08167
bone element6.26e-0882
anatomical conduit5.59e-07240


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
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.13.53539
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
MA0055.11.28887
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.15.61029
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.380957
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.114.5601
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.11.98562
MA0115.15.12834
MA0116.111.8178
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
MA0139.10.344952
MA0140.10.779643
MA0141.12.4958
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.24.65898
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.22.43626
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.16.35649
MA0155.12.30186
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.11.78721
MA0161.10
MA0162.10.0928415
MA0163.19.72701
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.6798
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#90534.752151182721970.01386206996689490.0487487617103015
ETS1#211337.296570691651750.00400857377511390.0192147712731376
ZBTB7A#5134135.513931980906920.009038352821081090.0342633949285259



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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