Personal tools

Coexpression cluster:C131: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:38, 17 September 2013


Full id: C131_lung_trachea_Alveolar_thyroid_umbilical_throat_skin



Phase1 CAGE Peaks

Hg19::chr10:24407319..24407323,-p@chr10:24407319..24407323
-
Hg19::chr10:24407447..24407471,+p@chr10:24407447..24407471
+
Hg19::chr10:97200772..97200774,-p@chr10:97200772..97200774
-
Hg19::chr11:12301789..12301797,+p@chr11:12301789..12301797
+
Hg19::chr11:128435202..128435212,+p@chr11:128435202..128435212
+
Hg19::chr11:128435216..128435219,+p@chr11:128435216..128435219
+
Hg19::chr11:19218255..19218267,+p1@ENST00000527978
Hg19::chr11:19218282..19218292,+p2@ENST00000527978
Hg19::chr11:19218311..19218319,+p3@ENST00000527978
Hg19::chr12:114843852..114843867,-p3@TBX5
Hg19::chr12:120151559..120151570,-p14@CIT
Hg19::chr12:9268819..9268829,-p10@A2M
Hg19::chr13:43321515..43321525,-p@chr13:43321515..43321525
-
Hg19::chr14:25479779..25479798,-p5@STXBP6
Hg19::chr14:36686942..36686967,-p@chr14:36686942..36686967
-
Hg19::chr14:36789763..36789774,-p3@MBIP
Hg19::chr14:36921583..36921586,+p@chr14:36921583..36921586
+
Hg19::chr14:36982998..36983015,-p5@SFTA3
Hg19::chr15:42565023..42565070,-p@chr15:42565023..42565070
-
Hg19::chr15:79286231..79286243,-p@chr15:79286231..79286243
-
Hg19::chr15:90542449..90542461,+p@chr15:90542449..90542461
+
Hg19::chr16:19404680..19404693,+p@chr16:19404680..19404693
+
Hg19::chr16:2379688..2379711,-p3@ABCA3
Hg19::chr16:53920795..53920815,+p3@FTO
Hg19::chr16:53920908..53920911,+p@chr16:53920908..53920911
+
Hg19::chr16:66167868..66167902,-p@chr16:66167868..66167902
-
Hg19::chr17:42923679..42923685,+p@chr17:42923679..42923685
+
Hg19::chr17:42923686..42923705,+p@chr17:42923686..42923705
+
Hg19::chr17:59479775..59479790,+p@chr17:59479775..59479790
+
Hg19::chr17:59529743..59529798,+p1@TBX4
Hg19::chr17:59533618..59533656,+p2@TBX4
Hg19::chr17:66539483..66539491,+p1@AK127041
Hg19::chr18:21242729..21242739,-p6@ANKRD29
Hg19::chr19:46800044..46800048,-p@chr19:46800044..46800048
-
Hg19::chr19:46800076..46800087,-p@chr19:46800076..46800087
-
Hg19::chr1:155972294..155972308,-p5@ENST00000454974
Hg19::chr1:155972346..155972351,-p3@ENST00000454974
Hg19::chr1:155972403..155972419,-p2@ENST00000454974
Hg19::chr1:170904671..170904677,+p4@C1orf129
Hg19::chr1:171157193..171157195,+p@chr1:171157193..171157195
+
Hg19::chr1:212241407..212241415,+p@chr1:212241407..212241415
+
Hg19::chr1:212241433..212241451,+p@chr1:212241433..212241451
+
Hg19::chr1:212241481..212241492,+p6@DTL
Hg19::chr1:242310809..242310817,+p@chr1:242310809..242310817
+
Hg19::chr1:39624527..39624560,+p@chr1:39624527..39624560
+
Hg19::chr1:61742889..61742902,+p@chr1:61742889..61742902
+
Hg19::chr1:62102759..62102782,+p@chr1:62102759..62102782
+
Hg19::chr20:41466192..41466207,-p@chr20:41466192..41466207
-
Hg19::chr20:41466212..41466225,-p@chr20:41466212..41466225
-
Hg19::chr20:45938947..45938951,-p@chr20:45938947..45938951
-
Hg19::chr20:58402101..58402106,+p@chr20:58402101..58402106
+
Hg19::chr2:100721923..100721930,-p16@AFF3
Hg19::chr2:167350586..167350598,-p6@SCN7A
Hg19::chr2:167350627..167350640,-p4@SCN7A
Hg19::chr2:167350641..167350689,-p1@SCN7A
Hg19::chr2:167350691..167350705,-p5@SCN7A
Hg19::chr2:167350710..167350728,-p3@SCN7A
Hg19::chr2:167350747..167350765,-p2@SCN7A
Hg19::chr2:173686338..173686351,+p8@RAPGEF4
Hg19::chr2:179184955..179185003,+p6@OSBPL6
Hg19::chr2:180426561..180426570,-p@chr2:180426561..180426570
-
Hg19::chr2:180426572..180426590,-p@chr2:180426572..180426590
-
Hg19::chr2:180426591..180426598,-p@chr2:180426591..180426598
-
Hg19::chr2:180427304..180427323,-p7@ZNF385B
Hg19::chr2:192214808..192214826,+p@chr2:192214808..192214826
+
Hg19::chr2:220131198..220131209,+p@chr2:220131198..220131209
+
Hg19::chr2:239478694..239478698,+p@chr2:239478694..239478698
+
Hg19::chr2:85893443..85893453,-p@chr2:85893443..85893453
-
Hg19::chr2:85893469..85893476,-p@chr2:85893469..85893476
-
Hg19::chr2:85893492..85893505,-p@chr2:85893492..85893505
-
Hg19::chr2:85893526..85893535,-p@chr2:85893526..85893535
-
Hg19::chr2:85893596..85893605,-p@chr2:85893596..85893605
-
Hg19::chr2:85893626..85893634,-p@chr2:85893626..85893634
-
Hg19::chr2:85893667..85893682,-p@chr2:85893667..85893682
-
Hg19::chr2:85893688..85893699,-p@chr2:85893688..85893699
-
Hg19::chr2:85893708..85893714,-p@chr2:85893708..85893714
-
Hg19::chr2:85893719..85893738,-p@chr2:85893719..85893738
-
Hg19::chr2:85893752..85893757,-p22@SFTPB
Hg19::chr2:85893907..85893914,-p16@SFTPB
Hg19::chr2:85894509..85894524,-p@chr2:85894509..85894524
-
Hg19::chr2:85894565..85894575,-p@chr2:85894565..85894575
-
Hg19::chr2:85894747..85894754,-p@chr2:85894747..85894754
-
Hg19::chr2:85894796..85894807,-p@chr2:85894796..85894807
-
Hg19::chr2:85894916..85894923,-p@chr2:85894916..85894923
-
Hg19::chr2:85894926..85894931,-p@chr2:85894926..85894931
-
Hg19::chr2:85895315..85895331,-p1@SFTPB
Hg19::chr3:137728947..137728952,+p6@CLDN18
Hg19::chr3:137728965..137728978,+p4@CLDN18
Hg19::chr3:137728985..137729022,+p1@CLDN18
Hg19::chr3:137729026..137729037,+p3@CLDN18
Hg19::chr3:137729095..137729097,+p10@CLDN18
Hg19::chr3:137729107..137729112,+p8@CLDN18
Hg19::chr3:150966861..150966873,-p6@P2RY14
Hg19::chr3:150966997..150967012,-p11@P2RY14
Hg19::chr3:151178921..151178926,-p@chr3:151178921..151178926
-
Hg19::chr3:193224569..193224573,+p@chr3:193224569..193224573
+
Hg19::chr3:44974953..44974981,-p12@ZDHHC3
Hg19::chr3:44975003..44975027,-p9@ZDHHC3
Hg19::chr3:74002015..74002023,-p@chr3:74002015..74002023
-
Hg19::chr4:152136458..152136467,-p@chr4:152136458..152136467
-
Hg19::chr4:189645023..189645058,-p@chr4:189645023..189645058
-
Hg19::chr4:41052963..41052979,-p@chr4:41052963..41052979
-
Hg19::chr4:62067299..62067303,+p24@LPHN3
Hg19::chr4:62067309..62067334,+p4@LPHN3
Hg19::chr4:89951028..89951062,-p20@FAM13A
Hg19::chr5:147258266..147258280,+p1@SCGB3A2
Hg19::chr5:58512790..58512799,-p@chr5:58512790..58512799
-
Hg19::chr5:59481406..59481413,-p97@PDE4D
Hg19::chr5:59481466..59481475,-p81@PDE4D
Hg19::chr5:59481477..59481489,-p54@PDE4D
Hg19::chr5:66786488..66786492,-p@chr5:66786488..66786492
-
Hg19::chr6:117746827..117746839,-p3@ROS1
Hg19::chr6:117746914..117746924,-p8@ROS1
Hg19::chr6:134210095..134210147,-p1@uc003qeg.1
Hg19::chr6:134212884..134212896,-p@chr6:134212884..134212896
-
Hg19::chr7:105603699..105603732,+p2@CDHR3
Hg19::chr7:105603738..105603753,+p4@CDHR3
Hg19::chr7:116165854..116165868,+p38@CAV1
Hg19::chr7:18329712..18329716,+p14@HDAC9
Hg19::chr7:22395904..22395928,+p@chr7:22395904..22395928
+
Hg19::chr7:24957750..24957761,-p8@OSBPL3
Hg19::chr7:37355939..37355973,-p@chr7:37355939..37355973
-
Hg19::chr7:80231640..80231661,+p5@CD36
Hg19::chr8:13017116..13017122,+p@chr8:13017116..13017122
+
Hg19::chr8:40019010..40019016,+p1@ENST00000520487
Hg19::chr8:55471739..55471763,+p2@RP1
Hg19::chr8:55471764..55471769,+p5@RP1
Hg19::chr8:55471773..55471782,+p4@RP1
Hg19::chr8:55471789..55471798,+p7@RP1
Hg19::chr9:112899329..112899346,+p37@AKAP2
Hg19::chr9:35237686..35237695,+p@chr9:35237686..35237695
+
Hg19::chr9:35237706..35237730,+p@chr9:35237706..35237730
+
Hg19::chr9:71926025..71926056,-p@chr9:71926025..71926056
-
Hg19::chr9:87493889..87493905,+p@chr9:87493889..87493905
+
Hg19::chrX:109003963..109003970,-p@chrX:109003963..109003970
-
Hg19::chrX:19649646..19649677,+p@chrX:19649646..19649677
+
Hg19::chrX:22050546..22050583,+p6@PHEX
Hg19::chrX:93977772..93977777,+p@chrX:93977772..93977777
+
Hg19::chrX:93977835..93977842,+p@chrX:93977835..93977842
+


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:0030326embryonic limb morphogenesis0.000413190761542128
GO:0035113embryonic appendage morphogenesis0.000413190761542128
GO:0048736appendage development0.000413190761542128
GO:0060173limb development0.000413190761542128
GO:0035107appendage morphogenesis0.000413190761542128
GO:0035108limb morphogenesis0.000413190761542128
GO:0000267cell fraction0.000812130961869082
GO:0048598embryonic morphogenesis0.005005689993078
GO:0006869lipid transport0.0133524163256075
GO:0032501multicellular organismal process0.0133524163256075
GO:0005624membrane fraction0.0144859017243564
GO:0007275multicellular organismal development0.0257074453471486
GO:0035110leg morphogenesis0.0257074453471486
GO:0010037response to carbon dioxide0.0257074453471486
GO:0060044negative regulation of cardiac muscle cell proliferation0.0257074453471486
GO:0000173inactivation of MAPK activity during osmolarity sensing0.0257074453471486
GO:0060039pericardium development0.0257074453471486
GO:0000161MAPKKK cascade during osmolarity sensing0.0257074453471486
GO:0009790embryonic development0.0318752593228725
GO:0048856anatomical structure development0.0355797311796446
GO:0042599lamellar body0.0355797311796446
GO:0060043regulation of cardiac muscle cell proliferation0.0355797311796446
GO:0051890regulation of cardioblast differentiation0.0355797311796446
GO:0051891positive regulation of cardioblast differentiation0.0355797311796446
GO:0007231osmosensory signaling pathway0.0355797311796446
GO:0045029UDP-activated nucleotide receptor activity0.0355797311796446
GO:0009605response to external stimulus0.0420308275413828
GO:0048731system development0.0420308275413828
GO:0019959interleukin-8 binding0.0420308275413828
GO:0015065uridine nucleotide receptor activity0.0420308275413828
GO:0035117embryonic arm morphogenesis0.0420308275413828
GO:0035140arm morphogenesis0.0420308275413828
GO:0017114wide-spectrum protease inhibitor activity0.0420308275413828
GO:0048513organ development0.0462420086398967



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><br>uberon_data<br><br>


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)
MA0003.14.44073e-14
MA0004.10.00024284
MA0006.10.179897
MA0007.10.0972622
MA0009.12.09439
MA0014.14.37318e-07
MA0017.10.299407
MA0019.10.134243
MA0024.10.481581
MA0025.10.319836
MA0027.11.30259
MA0028.10.0123605
MA0029.11.20932
MA0030.11.16255
MA0031.10.36705
MA0038.10.305883
MA0040.10.536845
MA0041.10.743387
MA0042.13.32834
MA0043.10.413916
MA0046.11.08098
MA0048.10.689351
MA0050.10.289724
MA0051.10.171923
MA0052.10.296653
MA0055.13.95478
MA0056.10
MA0057.10.0149943
MA0058.10.000238717
MA0059.10.180704
MA0060.17.61508e-06
MA0061.10.000950974
MA0063.10
MA0066.10.475457
MA0067.10.190212
MA0068.10.424146
MA0069.10.690798
MA0070.10.162859
MA0071.10.224745
MA0072.12.46871
MA0073.11.05416
MA0074.10.90428
MA0076.10.00681866
MA0077.10.633425
MA0078.10.0303426
MA0081.10.0314431
MA0083.10.74713
MA0084.10.313207
MA0087.10.646162
MA0088.15.21908e-06
MA0089.10
MA0090.10.0239612
MA0091.12.37186
MA0092.11.36334
MA0093.13.59406e-05
MA0095.10
MA0098.10
MA0100.10.0124164
MA0101.10.0223386
MA0103.10.436911
MA0105.10.000609743
MA0106.10.0559353
MA0107.10.000351653
MA0108.20.361271
MA0109.10
MA0111.10.299005
MA0113.11.96373
MA0114.10.119371
MA0115.10.885511
MA0116.10.202772
MA0117.11.25259
MA0119.10.600611
MA0122.10.895957
MA0124.10.398839
MA0125.10.299757
MA0130.10
MA0131.10.614642
MA0132.10
MA0133.10
MA0135.10.0584654
MA0136.10.095958
MA0139.10.000513953
MA0140.10.522947
MA0141.10.871302
MA0142.10.153597
MA0143.10.148737
MA0144.10.263435
MA0145.10.0295699
MA0146.10.000130642
MA0147.10.000115116
MA0148.14.85515
MA0149.11.80349
MA0062.21.0427e-06
MA0035.20.121483
MA0039.21.8256e-10
MA0138.20.354634
MA0002.20.474574
MA0137.20.102645
MA0104.20.000135403
MA0047.20.569495
MA0112.20.453886
MA0065.20.153202
MA0150.10.664421
MA0151.10
MA0152.10.546979
MA0153.10.994236
MA0154.10.226627
MA0155.10.00340068
MA0156.10.251524
MA0157.11.00092
MA0158.10
MA0159.10.0626499
MA0160.10.181672
MA0161.10
MA0162.11.78135e-10
MA0163.10.00730814
MA0164.10.993049
MA0080.20.649322
MA0018.20.410256
MA0099.20.0628944
MA0079.20
MA0102.20.340338
MA0258.11.91517
MA0259.10.0117208
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
SUZ12#2351282.88436149128420.007034816120237180.029353142660066



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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C131&oldid=3067249"