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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.524022667133446,

Latest revision as of 11:42, 17 September 2013


Full id: C1324_Fibroblast_Preadipocyte_basal_migratory_mesenchymal_Smooth_spindle



Phase1 CAGE Peaks

Hg19::chr10:95242223..95242232,-p8@MYOF
Hg19::chr18:56246303..56246344,-p9@ALPK2
Hg19::chr18:56246346..56246375,-p6@ALPK2
Hg19::chr18:56246399..56246415,-p15@ALPK2
Hg19::chr18:56246464..56246503,-p3@ALPK2
Hg19::chr4:77659857..77659874,+p3@SHROOM3


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:0043476pigment accumulation0.00447414122204642
GO:0043482cellular pigment accumulation0.00447414122204642
GO:0033059cellular pigmentation0.00447414122204642
GO:0045176apical protein localization0.00894736048387635
GO:0008105asymmetric protein localization0.00894736048387635
GO:0022603regulation of anatomical structure morphogenesis0.0234757577475775
GO:0008360regulation of cell shape0.0234757577475775
GO:0022604regulation of cell morphogenesis0.0234757577475775
GO:0005912adherens junction0.026824695916118
GO:0016324apical plasma membrane0.030395052708795
GO:0045177apical part of cell0.0349369160994711
GO:0007389pattern specification process0.0461504527999066



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>

Cell Type
Ontology termp-valuen
fibroblast4.37e-2276
skin fibroblast1.56e-1123
multi fate stem cell4.52e-10427
preadipocyte6.34e-1012
somatic stem cell2.57e-09433
mesothelial cell2.91e-0919
stem cell2.29e-08441
animal cell3.60e-08679
eukaryotic cell3.60e-08679
non-terminally differentiated cell1.90e-07106
motile cell9.29e-07386
Uber Anatomy
Ontology termp-valuen
integument4.62e-0946
integumental system4.62e-0946
skin of body9.31e-0941
dense mesenchyme tissue1.17e-0873
somite1.57e-0871
presomitic mesoderm1.57e-0871
presumptive segmental plate1.57e-0871
dermomyotome1.57e-0871
trunk paraxial mesoderm1.57e-0871
paraxial mesoderm3.10e-0872
presumptive paraxial mesoderm3.10e-0872
epithelial vesicle1.42e-0778
multilaminar epithelium4.48e-0783


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.262822
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
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.147053
MA0058.11.16137
MA0059.11.15845
MA0060.10.267412
MA0061.11.93637
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.12.3765
MA0084.11.5477
MA0087.11.00322
MA0088.11.61871
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.81721
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.14.2177
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
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
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.709311
MA0137.21.87543
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.21.52352
MA0079.25.9246e-06
MA0102.21.58513
MA0258.10.289793
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
STAT3#677458.766220830961874.28672496720299e-050.000765955977501647



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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