Personal tools

Coexpression cluster:C1421: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.815699384741068,0

Latest revision as of 11:44, 17 September 2013


Full id: C1421_Mesenchymal_Preadipocyte_Fibroblast_tenocyte_Adipocyte_Osteoblast_Nucleus



Phase1 CAGE Peaks

Hg19::chr16:4431722..4431771,+p@chr16:4431722..4431771
+
Hg19::chr19:14049136..14049171,-p2@PODNL1
Hg19::chr19:14049184..14049242,-p1@PODNL1
Hg19::chr1:1290954..1290971,-p8@MXRA8
Hg19::chr1:1293904..1293949,-p1@MXRA8
Hg19::chr21:47517478..47517529,+p9@COL6A2


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

GO IDGO nameFDR corrected p-value
GO:0005578proteinaceous extracellular matrix0.0118525173614682
GO:0044421extracellular region part0.0274556468016525
GO:0030198extracellular matrix organization and biogenesis0.0351588482143845
GO:0043062extracellular structure organization and biogenesis0.041676742962934
GO:0030674protein binding, bridging0.041676742962934
GO:0005201extracellular matrix structural constituent0.0467083833212877
GO:0006817phosphate transport0.0467083833212877



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 tissue3.41e-2273
paraxial mesoderm1.36e-2172
presumptive paraxial mesoderm1.36e-2172
somite1.39e-2171
presomitic mesoderm1.39e-2171
presumptive segmental plate1.39e-2171
dermomyotome1.39e-2171
trunk paraxial mesoderm1.39e-2171
epithelial vesicle2.80e-2178
skeletal muscle tissue1.28e-1862
striated muscle tissue1.28e-1862
myotome1.28e-1862
mesenchyme2.87e-18160
entire embryonic mesenchyme2.87e-18160
muscle tissue5.57e-1864
musculature5.57e-1864
musculature of body5.57e-1864
trunk mesenchyme1.55e-17122
multilaminar epithelium2.99e-1783
organism subdivision2.19e-13264
integument3.94e-1146
integumental system3.94e-1146
trunk4.04e-11199
multi-tissue structure4.70e-11342
surface structure7.48e-1199
unilaminar epithelium2.34e-09148
skin of body5.13e-0941
multi-cellular organism9.12e-09656
organ component layer9.36e-0966
tissue1.21e-08773
adipose tissue2.26e-0714
mesoderm6.74e-07315
mesoderm-derived structure6.74e-07315
presumptive mesoderm6.74e-07315


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)
MA0003.11.37104
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.11.45353
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.71708
MA0056.10
MA0057.12.74001
MA0058.11.16137
MA0059.11.15845
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.72313
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.19.66609
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.11.72264
MA0114.10.845337
MA0115.11.28169
MA0116.12.36812
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.13.00011
MA0146.14.09433
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.21.86512
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.22.25875
MA0065.22.35074
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.11.60937
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.18.07551
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.23.58629
MA0102.21.58513
MA0258.11.43672
MA0259.10.336472
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

No analysis results for this cluster

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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1421&oldid=3068538"