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Coexpression cluster:C502: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:24, 17 September 2013


Full id: C502_mesothelioma_Basophils_liposarcoma_Olfactory_Fibroblast_mesenchymal_CD14



Phase1 CAGE Peaks

Hg19::chr14:68569696..68569698,-p@chr14:68569696..68569698
-
Hg19::chr14:80012381..80012392,+p@chr14:80012381..80012392
+
Hg19::chr17:424957..424966,-p@chr17:424957..424966
-
Hg19::chr17:424968..425008,-p@chr17:424968..425008
-
Hg19::chr17:425023..425038,-p@chr17:425023..425038
-
Hg19::chr17:425199..425204,-p@chr17:425199..425204
-
Hg19::chr17:425270..425295,-p@chr17:425270..425295
-
Hg19::chr21:28941690..28941715,+p@chr21:28941690..28941715
+
Hg19::chr21:44888145..44888157,+p@chr21:44888145..44888157
+
Hg19::chr21:44888635..44888639,-p@chr21:44888635..44888639
-
Hg19::chr5:14145362..14145405,-p@chr5:14145362..14145405
-
Hg19::chr5:14145555..14145567,-p@chr5:14145555..14145567
-
Hg19::chr5:169035599..169035606,-p@chr5:169035599..169035606
-
Hg19::chr5:57104911..57104918,-p@chr5:57104911..57104918
-
Hg19::chr5:63585309..63585318,+p@chr5:63585309..63585318
+
Hg19::chr6:169562875..169562880,-p7@ENST00000439703
Hg19::chr9:81402959..81402971,-p@chr9:81402959..81402971
-
Hg19::chr9:81496646..81496675,+p@chr9:81496646..81496675
+
Hg19::chr9:81641483..81641491,-p@chr9:81641483..81641491
-


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><br><br>

Cell Type
Ontology termp-valuen
mesothelial cell6.95e-1219


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)
MA0003.13.71336e-06
MA0004.10.563888
MA0006.10.308609
MA0007.10.180248
MA0009.10.580032
MA0014.10.00255873
MA0017.10.114723
MA0019.10.305657
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.101383
MA0029.10.50258
MA0030.10.492344
MA0031.11.11067
MA0038.10.269828
MA0040.10.507819
MA0041.10.595574
MA0042.10.541224
MA0043.10.580321
MA0046.10.570066
MA0048.10.716475
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.66835
MA0056.10
MA0057.10.0434899
MA0058.10.407083
MA0059.10.805771
MA0060.10.0387582
MA0061.10.029485
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.10.409781
MA0069.10.566544
MA0070.10.556335
MA0071.10.240074
MA0072.10.552241
MA0073.118.557
MA0074.10.734236
MA0076.10.139892
MA0077.10.545231
MA0078.10.346453
MA0081.10.129245
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.126597
MA0089.10
MA0090.10.891785
MA0091.10.195166
MA0092.10.168981
MA0093.11.07718
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.0959778
MA0103.10.295078
MA0105.10.103598
MA0106.10.817478
MA0107.10.0591705
MA0108.20.432749
MA0109.10
MA0111.10.15804
MA0113.10.315797
MA0114.10.0569149
MA0115.10.805883
MA0116.10.0607301
MA0117.10.614633
MA0119.11.2467
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.10.0257123
MA0140.10.238066
MA0141.10.128074
MA0142.10.407878
MA0143.10.315941
MA0144.10.189563
MA0145.10.278749
MA0146.12.87274e-05
MA0147.10.223797
MA0148.10.606512
MA0149.10.230803
MA0062.20.027823
MA0035.20.237534
MA0039.20.00730638
MA0138.20.347473
MA0002.21.7902
MA0137.20.342218
MA0104.20.151208
MA0047.20.795472
MA0112.20.0184087
MA0065.20.0221473
MA0150.10.87566
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.10.0342743
MA0155.10.236629
MA0156.10.106343
MA0157.10.99963
MA0158.10
MA0159.10.062613
MA0160.10.222325
MA0161.10
MA0162.10.0505942
MA0163.10.000591497
MA0164.10.32594
MA0080.20.31321
MA0018.20.30364
MA0099.21.26491
MA0079.26.81553e-07
MA0102.21.09681
MA0258.10.046907
MA0259.10.235101
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.

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