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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:35, 17 September 2013


Full id: C1004_chorionic_pancreatic_choriocarcinoma_amniotic_placenta_colon_Placental



Phase1 CAGE Peaks

Hg19::chr11:7595176..7595189,+p19@PPFIBP2
Hg19::chr17:73982309..73982324,+p4@TEN1
Hg19::chr20:18125679..18125686,+p7@CSRP2BP
Hg19::chr20:18125727..18125755,+p4@CSRP2BP
Hg19::chr20:18125925..18125964,+p5@CSRP2BP
Hg19::chrX:52112136..52112150,+p3@XAGE2B
p3@XAGE2
Hg19::chrX:52112158..52112165,+p1@XAGE2B
p1@XAGE2
Hg19::chrX:52386980..52387013,-p2@XAGE2B
p2@XAGE2


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:0030274LIM domain binding0.0105961823506016
GO:0008907integrase activity0.0150088277864031
GO:0015074DNA integration0.0182422653092127
GO:0008080N-acetyltransferase activity0.0261641131540075
GO:0016407acetyltransferase activity0.0261641131540075
GO:0016410N-acyltransferase activity0.0261641131540075
GO:0019904protein domain specific binding0.0319837703946395
GO:0008415acyltransferase activity0.049075006499733
GO:0016747transferase activity, transferring groups other than amino-acyl groups0.049075006499733



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
extraembryonic membrane1.65e-6714
membranous layer1.65e-6714
chorion3.12e-477
extraembryonic structure1.77e-3824
placenta2.89e-274
allantois2.89e-274
amnion7.04e-247
acellular anatomical structure9.13e-223
egg chorion9.13e-223
somatic layer of lateral plate mesoderm6.99e-218
organ component layer5.40e-2066
uterus6.53e-1121
embryonic uterus2.16e-1022
internal female genitalia2.16e-1022
internal genitalia4.41e-0925
female reproductive organ5.97e-0837
female reproductive system5.97e-0837
epithelium of female gonad8.69e-081
rectum1.10e-074
reproductive organ1.14e-0748
reproductive structure1.17e-0759
reproductive system1.17e-0759
intestinal mucosa1.35e-074
wall of intestine1.35e-074
gastrointestinal system mucosa1.35e-074
gastrointestinal system epithelium1.35e-074
intestinal epithelium1.35e-074
female organism4.28e-0741
Disease
Ontology termp-valuen
islet cell tumor2.04e-081
endocrine pancreas cancer2.04e-081
pancreatic endocrine carcinoma2.04e-081
ovary epithelial cancer8.69e-081


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)
MA0003.10.00718652
MA0004.12.01344
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.134069
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.13.19039
MA0031.11.78748
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.11.56323
MA0058.13.50644
MA0059.12.54821
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.215282
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.15.02056
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.13.68539
MA0091.10.458301
MA0092.10.421159
MA0093.13.13688
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.792149
MA0105.10.0818021
MA0106.10.59853
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.00761723
MA0147.11.26392
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.44475
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.21.66814
MA0047.20.586412
MA0112.20.0572179
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.11.29801
MA0153.11.01778
MA0154.10.974997
MA0155.10.0535085
MA0156.10.323987
MA0157.11.66465
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.141536
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.200187
MA0102.21.46209
MA0258.10.209744
MA0259.10.699589
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
BHLHE40#8553211.21795338674440.0127147255611290.0458676115809038
HNF4A#317238.674608886107630.003838470874117280.0189392006246485
HNF4G#3174310.78253344741750.002064267375206250.0119712377366409



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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