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{{Coexpression_clusters
{
|full_id=C814_Alveolar_mesothelioma_bile_Renal_papillotubular_papillary_serous
|

Latest revision as of 11:31, 17 September 2013


Full id: C814_Alveolar_mesothelioma_bile_Renal_papillotubular_papillary_serous



Phase1 CAGE Peaks

Hg19::chr12:13044488..13044506,+p1@GPRC5A
Hg19::chr12:13061554..13061566,+p7@GPRC5A
Hg19::chr12:13061590..13061609,+p12@GPRC5A
Hg19::chr12:13061810..13061833,+p5@GPRC5A
Hg19::chr12:13061894..13061915,+p2@GPRC5A
Hg19::chr12:13065023..13065045,+p@chr12:13065023..13065045
+
Hg19::chr12:13065626..13065659,+p@chr12:13065626..13065659
+
Hg19::chr12:13065686..13065702,+p@chr12:13065686..13065702
+
Hg19::chr12:13065994..13066009,+p@chr12:13065994..13066009
+
Hg19::chr12:13068454..13068484,+p1@MIR614


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:0008067metabotropic glutamate, GABA-B-like receptor activity0.0259448957965383
GO:0008066glutamate receptor activity0.0259448957965383
GO:0030659cytoplasmic vesicle membrane0.0259448957965383
GO:0044433cytoplasmic vesicle part0.0259448957965383
GO:0012506vesicle membrane0.0259448957965383



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>

Cell Type
Ontology termp-valuen
epithelial cell1.07e-31253
mesothelial cell5.46e-1219
kidney cell1.51e-0717
kidney epithelial cell1.51e-0717
endo-epithelial cell2.07e-0742
squamous epithelial cell4.75e-0763
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.55e-13160
endoderm2.55e-13160
presumptive endoderm2.55e-13160
digestive system7.03e-12145
digestive tract7.03e-12145
primitive gut7.03e-12145
urinary system structure2.16e-1147
subdivision of digestive tract6.01e-11118
renal system6.72e-1148
respiratory primordium1.09e-0938
endoderm of foregut1.09e-0938
endo-epithelium2.59e-0982
epithelial bud4.11e-0937
respiratory tract6.59e-0954
larynx7.56e-099
prostate gland1.01e-0811
male accessory sex gland1.01e-0811
embryonic cloacal epithelium1.01e-0811
epithelium of hindgut1.01e-0811
urogenital sinus epithelium1.01e-0811
prostate bud1.01e-0811
prostate field1.01e-0811
trunk3.80e-08199
cloaca4.96e-0814
anal region4.96e-0814
embryonic cloaca4.96e-0814
terminal part of digestive tract4.96e-0814
primitive urogenital sinus4.96e-0814
proctodeum4.96e-0814
sex gland1.18e-0712
male reproductive gland1.18e-0712
organism subdivision1.24e-07264
trunk region element1.54e-07101
genitourinary system3.42e-0715
intermediate mesoderm5.21e-0728
Disease
Ontology termp-valuen
carcinoma2.59e-25106
cell type cancer1.64e-18143
disease of cellular proliferation1.28e-11239
adenocarcinoma2.51e-1025
cancer3.65e-10235
squamous cell carcinoma6.77e-0814


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
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.11.02846
MA0042.10.963243
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.014035
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.757837
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.11.11021e-05
MA0074.11.19015
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.79376
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.126492
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.189717
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
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
MA0141.11.43869
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.332712
MA0146.10.00275056
MA0147.10.184931
MA0148.11.04145
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.00259594
MA0138.20.569505
MA0002.20.80943
MA0137.20.710884
MA0104.20.138396
MA0047.20.504873
MA0112.20.573053
MA0065.20.147044
MA0150.11.52802
MA0151.10
MA0152.11.12912
MA0153.10.926242
MA0154.10.0494985
MA0155.10.030416
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.64451
MA0160.11.88551
MA0161.10
MA0162.10.108522
MA0163.10.0235237
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.22.14519e-05
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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
POLR2A#5430102.147453176558070.0004793377491637920.00436570639094072



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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