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{{Coexpression_clusters
{
|full_id=C172_chorionic_skeletal_tongue_amniotic_liver_gastrointestinal_Pericytes
 

Latest revision as of 10:48, 17 September 2013


Full id: C172_chorionic_skeletal_tongue_amniotic_liver_gastrointestinal_Pericytes



Phase1 CAGE Peaks

Hg19::chr11:2150745..2150785,+p1@BC127839
Hg19::chr11:2151798..2151813,-p2@IGF2
Hg19::chr11:2151877..2151902,+p@chr11:2151877..2151902
+
Hg19::chr11:2151947..2151958,+p@chr11:2151947..2151958
+
Hg19::chr11:2152575..2152590,+p@chr11:2152575..2152590
+
Hg19::chr11:2152641..2152652,+p@chr11:2152641..2152652
+
Hg19::chr11:2152665..2152693,+p27@IGF2
Hg19::chr11:2152702..2152747,+p17@IGF2
Hg19::chr11:2152775..2152817,+p14@IGF2
Hg19::chr11:2152829..2152834,+p57@IGF2
Hg19::chr11:2152856..2152896,+p21@IGF2
Hg19::chr11:2152902..2152970,+p13@IGF2
Hg19::chr11:2152974..2153103,+p10@IGF2
Hg19::chr11:2153071..2153082,-p8@IGF2
Hg19::chr11:2153108..2153139,+p29@IGF2
Hg19::chr11:2153157..2153189,+p26@IGF2
Hg19::chr11:2153165..2153178,-p11@IGF2
Hg19::chr11:2153201..2153247,+p18@IGF2
Hg19::chr11:2153253..2153337,+p15@IGF2
Hg19::chr11:2153332..2153354,-p6@IGF2
Hg19::chr11:2153356..2153374,-p7@IGF2
Hg19::chr11:2153389..2153416,-p4@IGF2
Hg19::chr11:2153449..2153463,-p5@IGF2
Hg19::chr11:2153576..2153579,-p@chr11:2153576..2153579
-
Hg19::chr11:2153590..2153601,-p@chr11:2153590..2153601
-
Hg19::chr11:2153605..2153619,-p@chr11:2153605..2153619
-
Hg19::chr11:2153817..2153828,+p3@BC075845
Hg19::chr11:2153850..2153861,+p2@BC075845
Hg19::chr11:2153890..2153941,+p1@BC075845
p2@BC021076
Hg19::chr11:2153950..2153990,+p1@BC021076
Hg19::chr11:2154002..2154014,+p3@BC021076
Hg19::chr11:2154041..2154052,+p4@BC021076
Hg19::chr11:2154088..2154099,+p5@CU674261
Hg19::chr11:2154095..2154106,-p@chr11:2154095..2154106
-
Hg19::chr11:2154106..2154118,+p3@CU674261
Hg19::chr11:2154122..2154138,+p4@CU674261
Hg19::chr11:2154145..2154155,+p7@CU674261
Hg19::chr11:2154203..2154221,+p2@CU674261
Hg19::chr11:2154248..2154285,+p1@CU674261
Hg19::chr11:2154382..2154391,+p6@CU674261
Hg19::chr11:2154762..2154797,+p@chr11:2154762..2154797
+
Hg19::chr11:2154767..2154781,-p36@IGF2
Hg19::chr11:2154790..2154814,-p24@IGF2
Hg19::chr11:2154832..2154852,-p44@IGF2
Hg19::chr11:2154872..2154893,-p38@IGF2
Hg19::chr11:2156633..2156657,-p32@IGF2
Hg19::chr11:2156660..2156669,-p64@IGF2
Hg19::chr11:2156671..2156708,-p40@IGF2
Hg19::chr11:2156713..2156749,-p37@IGF2
Hg19::chr11:2156751..2156773,-p55@IGF2
Hg19::chr11:2159479..2159489,-p54@IGF2
Hg19::chr11:2159491..2159532,-p23@IGF2
Hg19::chr11:2159538..2159595,-p12@IGF2
Hg19::chr11:2159572..2159583,+p20@BC017277
Hg19::chr11:2159607..2159615,-p1@X06260
Hg19::chr11:2159622..2159637,+p8@BC017277
Hg19::chr11:2159650..2159672,+p9@BC017277
Hg19::chr11:2159658..2159696,-p28@IGF2
Hg19::chr11:2159675..2159689,+p11@BC017277
Hg19::chr11:2159697..2159702,-p58@IGF2
Hg19::chr11:2159700..2159730,+p6@BC017277
Hg19::chr11:2159738..2159755,-p43@IGF2
Hg19::chr11:2159748..2159761,+p12@BC017277
Hg19::chr11:2159760..2159769,-p42@IGF2
Hg19::chr11:2159773..2159793,-p33@IGF2
Hg19::chr11:2159808..2159810,-p62@IGF2
Hg19::chr11:2159814..2159825,+p14@BC017277
Hg19::chr11:2159824..2159832,-p39@IGF2
Hg19::chr11:2159834..2159900,-p9@IGF2
Hg19::chr11:2159838..2159847,+p16@BC017277
Hg19::chr11:2159872..2159877,+p18@BC017277
Hg19::chr11:2159911..2159935,-p22@IGF2
Hg19::chr11:2159935..2159950,+p5@BC017277
Hg19::chr11:2159947..2159948,-p71@IGF2
Hg19::chr11:2159954..2159960,-p46@IGF2
Hg19::chr11:2159969..2159986,+p2@BC017277
Hg19::chr11:2159997..2160004,+p15@BC017277
Hg19::chr11:2160010..2160024,+p10@BC017277
Hg19::chr11:2160019..2160028,-p48@IGF2
Hg19::chr11:2160036..2160049,+p7@BC017277
Hg19::chr11:2160043..2160076,-p25@IGF2
Hg19::chr11:2160078..2160088,-p52@IGF2
Hg19::chr11:2160094..2160100,-p53@IGF2
Hg19::chr11:2160098..2160115,+p4@BC017277
Hg19::chr11:2160117..2160121,-p30@IGF2
Hg19::chr11:2160161..2160172,-p34@IGF2
Hg19::chr11:2160180..2160257,-p19@IGF2
Hg19::chr11:2160283..2160292,+p19@BC017277
Hg19::chr11:2160293..2160310,+p3@BC017277
Hg19::chr11:2160337..2160349,+p13@BC017277
Hg19::chr11:2160354..2160387,+p1@BC017277
Hg19::chr11:2160369..2160383,-p20@IGF2
Hg19::chr11:2160430..2160435,-p41@IGF2
Hg19::chr11:2160468..2160486,-p35@IGF2
Hg19::chr11:2160485..2160488,+p21@BC017277
Hg19::chr11:2160500..2160515,-p47@IGF2
Hg19::chr11:2160520..2160531,-p50@IGF2
Hg19::chr11:2160538..2160549,-p45@IGF2
Hg19::chr11:2160567..2160571,-p51@IGF2
Hg19::chr11:2160611..2160656,-p1@IGF2
Hg19::chr11:2162486..2162497,-p56@IGF2


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:0006349genetic imprinting0.00323796067349582
GO:0018445prothoracicotrophic hormone activity0.00323796067349582
GO:0005159insulin-like growth factor receptor binding0.00323796067349582
GO:0008286insulin receptor signaling pathway0.00582832921229247
GO:0005184neuropeptide hormone activity0.00582832921229247
GO:0040029regulation of gene expression, epigenetic0.00956670198987401
GO:0001501skeletal development0.0212920444287452
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0212920444287452
GO:0005179hormone activity0.0212920444287452
GO:0008083growth factor activity0.0223419286471212
GO:0007167enzyme linked receptor protein signaling pathway0.024084005009473



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 cell2.49e-1219
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane4.78e-1414
membranous layer4.78e-1414
extraembryonic structure8.88e-1224
endoderm-derived structure1.62e-11160
endoderm1.62e-11160
presumptive endoderm1.62e-11160
multi-tissue structure2.65e-10342
mesenchyme6.22e-10160
entire embryonic mesenchyme6.22e-10160
chorion3.11e-097
organ system subdivision2.95e-08223
multi-cellular organism2.43e-07656
digestive system2.54e-07145
digestive tract2.54e-07145
primitive gut2.54e-07145
intestine3.95e-0717
adult organism7.34e-07114


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)
MA0003.14.78404
MA0004.10.0122896
MA0006.18.347
MA0007.10.0336911
MA0009.10.0955291
MA0014.112.3141
MA0017.10.594403
MA0019.10.0116879
MA0024.10.0563848
MA0025.10.161182
MA0027.11.43827
MA0028.11.08791
MA0029.10.0627354
MA0030.10.0589208
MA0031.10.0400131
MA0038.11.24364
MA0040.10.857762
MA0041.10.0155809
MA0042.10.924034
MA0043.10.0956642
MA0046.10.0909318
MA0048.10.039907
MA0050.11.53089
MA0051.10.00694795
MA0052.10.0660788
MA0055.14.97984e-09
MA0056.10
MA0057.115.4483
MA0058.10.0326375
MA0059.10.0726493
MA0060.10.0438975
MA0061.10.068602
MA0063.10
MA0066.10.410039
MA0067.10.276424
MA0068.190.954
MA0069.10.0893328
MA0070.10.0847761
MA0071.11.36901
MA0072.13.33105
MA0073.178.3928
MA0074.10.00688893
MA0076.10.0407844
MA0077.10.0799522
MA0078.10.0184217
MA0081.10.000319784
MA0083.10.0987699
MA0084.11.06883
MA0087.10.989986
MA0088.10.0193825
MA0089.10
MA0090.10.0492872
MA0091.15.9545
MA0092.10.00105812
MA0093.10.00347683
MA0095.10
MA0098.10
MA0100.10.0436657
MA0101.10.00373648
MA0103.10.0522345
MA0105.14.51837
MA0106.10.0112489
MA0107.10.0170798
MA0108.21.4121
MA0109.10
MA0111.12.25419
MA0113.11.56672
MA0114.13.99608
MA0115.10.225497
MA0116.10.018469
MA0117.10.361412
MA0119.10.633293
MA0122.10.12468
MA0124.10.199604
MA0125.16.16623
MA0130.10
MA0131.112.5855
MA0132.10
MA0133.10
MA0135.10.108976
MA0136.10.00787796
MA0139.14.65722
MA0140.10.506014
MA0141.10.000306759
MA0142.10.131082
MA0143.10.558934
MA0144.10.296439
MA0145.10.00748713
MA0146.111.5052
MA0147.10.00811318
MA0148.10.00272859
MA0149.10.00392633
MA0062.20.0969197
MA0035.20.00440862
MA0039.20.58957
MA0138.20.0186149
MA0002.27.45364e-06
MA0137.20.364672
MA0104.20.0106253
MA0047.20.00995256
MA0112.24.26972
MA0065.210.5256
MA0150.10.00419758
MA0151.10
MA0152.10.329125
MA0153.10.142486
MA0154.10.706024
MA0155.10.589203
MA0156.10.00548501
MA0157.10.50252
MA0158.10
MA0159.10.558763
MA0160.10.0201511
MA0161.10
MA0162.18.92692
MA0163.144.2634
MA0164.10.0147973
MA0080.20.0298392
MA0018.20.517554
MA0099.20.329902
MA0079.2148.983
MA0102.20.445975
MA0258.10.0693724
MA0259.12.6029
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
FOSL2#2355162.682011976960270.0002844783653761130.00302613933606802
HEY1#23462873.480095650992051.67519531429499e-389.15998551987718e-36



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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