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{{Coexpression_clusters
{
|full_id=C227_chorionic_amniotic_Mesenchymal_Placental_gastric_diaphragm_tongue
|

Latest revision as of 11:01, 17 September 2013


Full id: C227_chorionic_amniotic_Mesenchymal_Placental_gastric_diaphragm_tongue



Phase1 CAGE Peaks

Hg19::chr11:2016471..2016492,+p3@RPSA
Hg19::chr11:2016512..2016519,-p10@BC106079
Hg19::chr11:2016522..2016560,-p1@BC106079
Hg19::chr11:2016652..2016663,-p9@BC106079
Hg19::chr11:2016663..2016681,+p5@RPSA
Hg19::chr11:2016672..2016677,-p11@BC106079
Hg19::chr11:2016689..2016722,-p3@BC106079
Hg19::chr11:2016732..2016739,-p8@BC106079
Hg19::chr11:2016740..2016751,-p7@BC106079
Hg19::chr11:2016752..2016772,-p5@BC106079
Hg19::chr11:2016780..2016789,-p2@AF116709
Hg19::chr11:2016791..2016794,-p1@AF116709
Hg19::chr11:2016803..2016860,-p4@H19
Hg19::chr11:2016865..2016913,-p9@H19
Hg19::chr11:2016915..2016943,-p24@H19
Hg19::chr11:2016937..2016981,+p@chr11:2016937..2016981
+
Hg19::chr11:2016952..2016959,-p35@H19
Hg19::chr11:2016960..2016996,-p20@H19
Hg19::chr11:2017005..2017026,-p27@H19
Hg19::chr11:2017110..2017135,+p@chr11:2017110..2017135
+
Hg19::chr11:2017138..2017174,-p18@H19
Hg19::chr11:2017178..2017212,-p16@H19
Hg19::chr11:2017214..2017227,-p10@H19
Hg19::chr11:2017228..2017236,-p34@H19
Hg19::chr11:2017331..2017342,-p30@H19
Hg19::chr11:2017349..2017365,-p7@H19
Hg19::chr11:2017366..2017393,-p3@H19
Hg19::chr11:2017367..2017398,+p@chr11:2017367..2017398
+
Hg19::chr11:2017395..2017407,-p17@H19
Hg19::chr11:2017416..2017437,-p13@H19
Hg19::chr11:2017525..2017553,+p@chr11:2017525..2017553
+
Hg19::chr11:2017623..2017638,-p14@H19
Hg19::chr11:2017656..2017665,-p36@H19
Hg19::chr11:2017849..2017895,+p@chr11:2017849..2017895
+
Hg19::chr11:2017862..2017869,-p28@H19
Hg19::chr11:2017907..2017914,-p32@H19
Hg19::chr11:2017929..2017975,+p@chr11:2017929..2017975
+
Hg19::chr11:2018007..2018012,-p1@MIR675
Hg19::chr11:2018058..2018067,+p14@AF118081
Hg19::chr11:2018115..2018182,+p4@AF118081
Hg19::chr11:2018178..2018183,-p31@H19
Hg19::chr11:2018235..2018266,+p7@AF118081
Hg19::chr11:2018305..2018318,-p8@H19
Hg19::chr11:2018321..2018332,-p22@H19
Hg19::chr11:2018359..2018371,-p11@H19
Hg19::chr11:2018389..2018396,-p26@H19
Hg19::chr11:2018395..2018415,+p9@AF118081
Hg19::chr11:2018399..2018408,-p23@H19
Hg19::chr11:2018440..2018456,-p5@H19
Hg19::chr11:2018455..2018516,+p2@AF118081
Hg19::chr11:2018467..2018477,-p19@H19
Hg19::chr11:2018544..2018555,-p21@H19
Hg19::chr11:2018636..2018661,+p6@AF118081
Hg19::chr11:2018694..2018745,+p3@AF118081
Hg19::chr11:2018773..2018785,-p12@H19
Hg19::chr11:2018875..2018886,-p25@H19
Hg19::chr11:2018901..2018914,-p6@H19
Hg19::chr11:2018956..2018969,-p15@H19
Hg19::chr11:2018977..2019048,-p1@H19
Hg19::chr11:2150461..2150472,+p5@BC104421
Hg19::chr11:2160324..2160330,+p17@BC017277
Hg19::chr11:2160680..2160696,-p59@IGF2
Hg19::chr1:2066627..2066640,+p19@PRKCZ


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

p.valueFDRnGenesnPathwayName
1.2723518646306e-050.008053987303111713312Diabetes pathways (Reactome):REACT_15380



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:0005055laminin receptor activity0.0172190497820848
GO:0004700atypical protein kinase C activity0.0172190497820848
GO:0006349genetic imprinting0.0229553539426068
GO:0018445prothoracicotrophic hormone activity0.0229553539426068
GO:0005159insulin-like growth factor receptor binding0.0245899540279904
GO:0004697protein kinase C activity0.0245899540279904
GO:0001565phorbol ester receptor activity0.0245899540279904
GO:0008286insulin receptor signaling pathway0.0389942395441504
GO:0005184neuropeptide hormone activity0.0389942395441504
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0389942395441504
GO:0007165signal transduction0.0409608036317618
GO:0007154cell communication0.0474708623037988
GO:0008305integrin complex0.0482976234877922
GO:0019992diacylglycerol binding0.0482976234877922
GO:0040029regulation of gene expression, epigenetic0.0496531872163847



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><br>

Cell Type
Ontology termp-valuen
extraembryonic cell1.86e-1219
cell of skeletal muscle1.39e-089
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane1.11e-1514
membranous layer1.11e-1514
larynx9.60e-149
upper respiratory tract5.82e-1319
extraembryonic structure2.27e-1224
chorion1.37e-117
endoderm-derived structure4.76e-09160
endoderm4.76e-09160
presumptive endoderm4.76e-09160
subdivision of digestive tract5.39e-09118
foregut7.78e-0987
multi-tissue structure3.81e-08342
digestive system7.44e-08145
digestive tract7.44e-08145
primitive gut7.44e-08145
mesenchyme9.16e-08160
entire embryonic mesenchyme9.16e-08160
placenta2.17e-074
allantois2.17e-074
segment of respiratory tract3.41e-0747
organ component layer7.07e-0766
organism subdivision9.44e-07264


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)
MA0003.13.19235
MA0004.15.52732
MA0006.10.508799
MA0007.10.0122757
MA0009.10.196219
MA0014.17.28873
MA0017.10.448072
MA0019.10.0476913
MA0024.10.136013
MA0025.10.285416
MA0027.11.64023
MA0028.11.08523
MA0029.10.146371
MA0030.10.140185
MA0031.10.10769
MA0038.10.140379
MA0040.10.149577
MA0041.10.0176845
MA0042.10.0129646
MA0043.10.196415
MA0046.10.189523
MA0048.10.828421
MA0050.10.0130821
MA0051.10.0340651
MA0052.10.151713
MA0055.10.571775
MA0056.10
MA0057.13.99405
MA0058.12.63085
MA0059.11.39408
MA0060.10.0846505
MA0061.10.0524823
MA0063.10
MA0066.11.34114
MA0067.10.426099
MA0068.10.953272
MA0069.10.187175
MA0070.10.180428
MA0071.10.0261486
MA0072.10.177746
MA0073.114.1573
MA0074.10.582101
MA0076.10.586105
MA0077.10.173186
MA0078.10.0642227
MA0081.10.329859
MA0083.10.200894
MA0084.10.58417
MA0087.10.176294
MA0088.15.17349
MA0089.10
MA0090.10.408906
MA0091.10.601808
MA0092.10.750287
MA0093.18.42348
MA0095.10
MA0098.10
MA0100.12.98956
MA0101.10.00203579
MA0103.10.30571
MA0105.10.956082
MA0106.10.0465186
MA0107.10.000468407
MA0108.20.106251
MA0109.10
MA0111.11.32363
MA0113.11.14665
MA0114.10.783087
MA0115.10.365583
MA0116.10.0951859
MA0117.10.22006
MA0119.10.292077
MA0122.11.24147
MA0124.10.333911
MA0125.10.272745
MA0130.10
MA0131.10.0709376
MA0132.10
MA0133.10
MA0135.10.215386
MA0136.10.612857
MA0139.10.323902
MA0140.10.0255919
MA0141.10.763768
MA0142.10.0932211
MA0143.10.0516412
MA0144.11.75041
MA0145.13.26229
MA0146.115.1464
MA0147.17.35443
MA0148.10.0187432
MA0149.10.0236308
MA0062.21.31048
MA0035.20.0254456
MA0039.20.361846
MA0138.20.0646653
MA0002.20.0696415
MA0137.20.0164711
MA0104.25.26904
MA0047.20.042965
MA0112.21.12912
MA0065.20.0217599
MA0150.10.104809
MA0151.10
MA0152.10.0269807
MA0153.10.260996
MA0154.10.0825928
MA0155.12.0634
MA0156.10.0169842
MA0157.10.0816079
MA0158.10
MA0159.16.2284
MA0160.10.0214458
MA0161.10
MA0162.10.0658274
MA0163.18.30132
MA0164.10.055624
MA0080.20.742931
MA0018.20.707077
MA0099.20.814242
MA0079.24.97698
MA0102.20.616902
MA0258.10.00194599
MA0259.16.41944
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
EGR1#1958231.821081256835450.001803058739523370.0109089127387951



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

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