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

Latest revision as of 12:06, 17 September 2013


Full id: C2478_testicular_chorionic_placenta_anaplastic_amniotic_choriocarcinoma_Placental



Phase1 CAGE Peaks

Hg19::chr19:1584937..1584949,-p1@M77818
Hg19::chr19:1584956..1584968,-p2@M77818
Hg19::chr3:49506374..49506387,+p15@DAG1
Hg19::chr7:97984753..97984783,-p9@BAIAP2L1


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:0002011morphogenesis of an epithelial sheet0.00423872249338194
GO:0005055laminin receptor activity0.00423872249338194
GO:0016011dystroglycan complex0.0112995998696127
GO:0042383sarcolemma0.0112995998696127
GO:0009653anatomical structure morphogenesis0.0112995998696127
GO:0005626insoluble fraction0.0112995998696127
GO:0016010dystrophin-associated glycoprotein complex0.0112995998696127
GO:0046847filopodium formation0.0112995998696127
GO:0030035microspike biogenesis0.0112995998696127
GO:0005605basal lamina0.0169454069541581
GO:0045121lipid raft0.0176488660653594
GO:0030031cell projection biogenesis0.0176488660653594
GO:0048856anatomical structure development0.0190571256358965
GO:0002009morphogenesis of an epithelium0.0190571256358965
GO:0005604basement membrane0.0208888706484029
GO:0044420extracellular matrix part0.0346386466874561
GO:0016043cellular component organization and biogenesis0.0349345137723753
GO:0003012muscle system process0.0349345137723753
GO:0006936muscle contraction0.0349345137723753
GO:0032502developmental process0.0349345137723753
GO:0032990cell part morphogenesis0.0374838474864422
GO:0030030cell projection organization and biogenesis0.0374838474864422
GO:0048858cell projection morphogenesis0.0374838474864422
GO:0032501multicellular organismal process0.0379629128886618
GO:0015629actin cytoskeleton0.0499693031959513



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
germ line cell2.02e-297
germ cell2.02e-297
chorionic membrane mesenchymal stem cell1.63e-183
extraembryonic cell1.92e-1819
amniotic epithelial cell1.58e-122
Disease
Ontology termp-valuen
heart disease2.49e-122
germ cell and embryonal cancer5.72e-0922
germ cell cancer5.72e-0922
vascular disease4.51e-071
ischemia4.51e-071
extrinsic cardiomyopathy4.51e-071
myocardial ischemia4.51e-071
myocardial infarction4.51e-071


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)
MA0003.11.45381
MA0004.10.71247
MA0006.11.31813
MA0007.11.65296
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.8712
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.11.8408
MA0072.11.1744
MA0073.10.00636811
MA0074.11.91637
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.24.78886
MA0099.20.7872
MA0079.20.20937
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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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