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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:32, 17 September 2013


Full id: C860_serous_mesothelioma_Renal_clear_colon_endometrial_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr6:24178711..24178718,-p@chr6:24178711..24178718
-
Hg19::chr6:24178792..24178829,+p@chr6:24178792..24178829
+
Hg19::chr6:24278432..24278446,-p@chr6:24278432..24278446
-
Hg19::chr6:24345366..24345371,-p@chr6:24345366..24345371
-
Hg19::chr6:24358088..24358099,-p5@DCDC2
Hg19::chr6:24358114..24358125,-p4@DCDC2
Hg19::chr6:24358146..24358176,-p1@DCDC2
Hg19::chr6:24358196..24358199,-p8@DCDC2
Hg19::chr6:24358226..24358239,-p3@DCDC2
Hg19::chr6:24358264..24358295,-p2@DCDC2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
abdomen element1.14e-2454
abdominal segment element1.14e-2454
kidney8.88e-2426
kidney mesenchyme8.88e-2426
upper urinary tract8.88e-2426
kidney rudiment8.88e-2426
kidney field8.88e-2426
nephron tubule epithelium2.61e-2210
abdominal segment of trunk2.35e-2160
abdomen2.35e-2160
cavitated compound organ4.45e-1931
excretory tube7.67e-1916
kidney epithelium7.67e-1916
trunk region element8.34e-18101
subdivision of trunk1.76e-17112
nephron epithelium6.60e-1715
renal tubule6.60e-1715
nephron tubule6.60e-1715
nephron6.60e-1715
uriniferous tubule6.60e-1715
nephrogenic mesenchyme6.60e-1715
urinary system structure1.13e-1347
renal system2.84e-1348
cortex of kidney2.36e-1112
renal parenchyma2.36e-1112
cortex4.77e-1115
parenchyma9.60e-0915
renal cortex tubule7.04e-083
region of nephron tubule7.04e-083
proximal tubule7.04e-083
compound organ1.01e-0768
endo-epithelium1.28e-0782
endocrine gland1.55e-0735
immaterial anatomical entity2.06e-07117
gut epithelium2.74e-0754
trunk2.94e-07199
thyroid gland4.36e-075
pharyngeal pouch4.36e-075
thyroid diverticulum4.36e-075
pharyngeal pouch 24.36e-075
thyroid primordium4.36e-075
Disease
Ontology termp-valuen
adenocarcinoma9.39e-1525
reproductive organ cancer1.01e-1129
female reproductive organ cancer5.78e-1127
cell type cancer8.42e-11143
carcinoma1.88e-10106
cancer2.15e-08235
disease of cellular proliferation5.52e-08239
disease of anatomical entity7.74e-0839


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)
MA0003.10.0586157
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.0036779
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.12.7903
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.13.17924
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.12.65966
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.11.12112
MA0072.10.798564
MA0073.10.0447366
MA0074.10.4723
MA0076.11.50024
MA0077.10.790956
MA0078.10.568317
MA0081.10.79376
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.11.20737
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.885497
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.10.437738
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.491079
MA0145.10.0359093
MA0146.10.128432
MA0147.10.184931
MA0148.11.04145
MA0149.10.428597
MA0062.21.77242
MA0035.20.437071
MA0039.20.000314573
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.0329985
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.10.12484
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.11.07255
MA0161.10
MA0162.10.0377269
MA0163.10.00405048
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.26.65357e-08
MA0102.21.36707
MA0258.10.155735
MA0259.11.06648
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
CEBPB#105164.782688575494890.0005200755356730160.0045060700904392
CTCF#1066463.216153823845020.004429095326154860.0209706359039028
GABPB1#255364.24061030170930.001006578916106460.00721177851541763
HDAC2#306668.049372141975762.76518202234458e-050.000584719265502421
MYC#460963.133369122965640.005077423268455520.0236310609952864
TCF7L2#693466.462105937882419.65893777244962e-050.00137509514996846



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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