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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.419763329820918,

Latest revision as of 11:24, 17 September 2013


Full id: C519_Preadipocyte_Ewing_Myoblast_spindle_Fibroblast_Adipocyte_Osteoblast



Phase1 CAGE Peaks

Hg19::chr6:35181725..35181742,+p3@SCUBE3
Hg19::chr6:35181783..35181815,+p2@SCUBE3
Hg19::chr6:35181816..35181850,+p1@SCUBE3
Hg19::chr6:35181866..35181878,+p7@SCUBE3
Hg19::chr6:35181935..35181948,+p4@SCUBE3
Hg19::chr6:35181964..35181980,+p5@SCUBE3
Hg19::chr6:35182176..35182190,+p6@SCUBE3
Hg19::chr6:35200689..35200695,+p9@SCUBE3
Hg19::chr6:35211380..35211391,+p@chr6:35211380..35211391
+
Hg19::chr6:35214004..35214032,+p@chr6:35214004..35214032
+
Hg19::chr6:35216360..35216374,+p10@SCUBE3
Hg19::chr6:35217101..35217114,+p@chr6:35217101..35217114
+
Hg19::chr6:35218080..35218089,+p@chr6:35218080..35218089
+
Hg19::chr6:35218158..35218175,+p@chr6:35218158..35218175
+
Hg19::chr6:35218350..35218364,+p2@AK123742
Hg19::chr6:35218435..35218446,+p4@AK123742
Hg19::chr6:35218509..35218513,+p1@AK123742
Hg19::chr6:35219318..35219336,+p3@AK123742


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:0048196middle lamella-containing extracellular matrix0.000183975038266808
GO:0009505cellulose and pectin-containing cell wall0.000183975038266808
GO:0048222glycoprotein network0.000183975038266808
GO:0009530primary cell wall0.000183975038266808
GO:0005618cell wall0.000294360061226893
GO:0044462external encapsulating structure part0.000490600102044821
GO:0030312external encapsulating structure0.000630771559771913
GO:0051291protein heterooligomerization0.000735900153067232
GO:0051260protein homooligomerization0.00335243403063961
GO:0051259protein oligomerization0.00456258094901684
GO:0044420extracellular matrix part0.00876390182289157
GO:0009986cell surface0.00907610188782919
GO:0006461protein complex assembly0.0192466193879122
GO:0065003macromolecular complex assembly0.0397386082656305
GO:0022607cellular component assembly0.0398857882962439



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
preadipocyte1.28e-1412
fibroblast6.81e-1376
skin fibroblast8.98e-1323
cell of skeletal muscle2.39e-109
multi fate stem cell3.11e-09427
connective tissue cell8.18e-09361
somatic stem cell8.48e-09433
stem cell1.20e-08441
fat cell2.89e-0815
stromal cell7.83e-0828
mesenchymal cell3.23e-07354
preadipocyte of the breast9.15e-073


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)
MA0003.10.149367
MA0004.10.207008
MA0006.10.101986
MA0007.10.193512
MA0009.10.600198
MA0014.10.0316187
MA0017.10.395274
MA0019.10.861701
MA0024.10.50459
MA0025.10.725013
MA0027.12.18072
MA0028.10.111328
MA0029.10.522011
MA0030.10.511665
MA0031.10.454061
MA0038.10.285594
MA0040.10.527306
MA0041.10.220669
MA0042.10.197306
MA0043.10.60049
MA0046.10.590147
MA0048.10.305316
MA0050.10.197941
MA0051.10.282227
MA0052.10.530811
MA0055.10.0623184
MA0056.10
MA0057.13.28491
MA0058.10.141262
MA0059.10.140431
MA0060.10.0444001
MA0061.12.2921
MA0063.10
MA0066.10.285934
MA0067.10.900956
MA0068.10.0222576
MA0069.10.586593
MA0070.11.41126
MA0071.10.255111
MA0072.10.572162
MA0073.16.50173e-05
MA0074.10.770086
MA0076.10.151641
MA0077.10.565087
MA0078.10.363755
MA0081.10.855093
MA0083.10.607144
MA0084.11.08294
MA0087.10.569916
MA0088.10.149441
MA0089.10
MA0090.10.161293
MA0091.10.601165
MA0092.10.53622
MA0093.10.103729
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.10.343779
MA0103.10.320022
MA0105.13.59878
MA0106.10.319
MA0107.11.31477
MA0108.20.451357
MA0109.10
MA0111.10.508569
MA0113.10.332535
MA0114.10.228885
MA0115.10.827474
MA0116.10.240715
MA0117.10.635078
MA0119.10.130226
MA0122.10.659244
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.10.379172
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.10.291242
MA0139.10.541807
MA0140.10.253051
MA0141.10.139313
MA0142.10.426146
MA0143.10.332682
MA0144.10.459643
MA0145.11.3651
MA0146.10.161375
MA0147.10.245602
MA0148.10.225411
MA0149.10.687248
MA0062.20.0323736
MA0035.20.252505
MA0039.20.0782174
MA0138.20.364793
MA0002.20.155585
MA0137.20.368913
MA0104.20.0440964
MA0047.20.309071
MA0112.20.160258
MA0065.20.772018
MA0150.10.157331
MA0151.10
MA0152.10.258148
MA0153.10.692238
MA0154.10.117204
MA0155.10.146881
MA0156.10.116546
MA0157.10.402372
MA0158.10
MA0159.10.0701863
MA0160.10.236884
MA0161.10
MA0162.10.214564
MA0163.11.06374
MA0164.11.62636
MA0080.20.338854
MA0018.20.320136
MA0099.20.716923
MA0079.27.2257
MA0102.21.11935
MA0258.10.053266
MA0259.10.0740439
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
ZNF263#1012773.197382858837490.003680521637022780.0185713595153649



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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