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Coexpression cluster:C128: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 10:38, 17 September 2013


Full id: C128_testicular_choriocarcinoma_H9_teratocarcinoma_pancreatic_iPS_HES3GFP



Phase1 CAGE Peaks

Hg19::chr10:135043702..135043729,+p1@UTF1
Hg19::chr10:135043750..135043761,+p6@UTF1
Hg19::chr10:135044006..135044017,+p12@UTF1
Hg19::chr10:135044123..135044144,+p5@UTF1
Hg19::chr10:135044466..135044478,+p@chr10:135044466..135044478
+
Hg19::chr10:135044532..135044541,+p@chr10:135044532..135044541
+
Hg19::chr10:135044555..135044569,+p@chr10:135044555..135044569
+
Hg19::chr11:107782394..107782402,+p@chr11:107782394..107782402
+
Hg19::chr11:69590101..69590112,-p1@FGF4
Hg19::chr12:10183309..10183314,+p4@CLEC9A
Hg19::chr12:12201285..12201324,-p@chr12:12201285..12201324
-
Hg19::chr12:123215761..123215801,-p3@HCAR1
Hg19::chr12:123590088..123590118,-p7@PITPNM2
Hg19::chr12:13014152..13014163,+p@chr12:13014152..13014163
+
Hg19::chr12:19592405..19592492,+p2@AEBP2
Hg19::chr12:23908625..23908650,-p@chr12:23908625..23908650
-
Hg19::chr12:24967393..24967404,-p28@BCAT1
Hg19::chr12:25054930..25054940,-p34@BCAT1
Hg19::chr12:25054986..25054996,-p30@BCAT1
Hg19::chr12:25055009..25055022,-p14@BCAT1
Hg19::chr12:25055037..25055054,-p11@BCAT1
Hg19::chr12:25055065..25055076,-p16@BCAT1
Hg19::chr12:25055107..25055119,-p9@BCAT1
Hg19::chr12:25055145..25055171,-p6@BCAT1
Hg19::chr12:25055177..25055258,-p5@BCAT1
Hg19::chr12:25055949..25056088,-p2@BCAT1
Hg19::chr12:25056096..25056116,-p13@BCAT1
Hg19::chr12:25056133..25056148,-p20@BCAT1
Hg19::chr12:32259576..32259585,+p5@BICD1
Hg19::chr12:32259603..32259610,+p7@BICD1
Hg19::chr12:32259696..32259794,+p1@BICD1
Hg19::chr12:32259802..32259816,+p2@BICD1
Hg19::chr12:32259821..32259835,+p4@BICD1
Hg19::chr12:32288349..32288353,+p@chr12:32288349..32288353
+
Hg19::chr12:32480585..32480601,+p@chr12:32480585..32480601
+
Hg19::chr12:32552269..32552321,+p9@FGD4
Hg19::chr12:32552586..32552593,+p18@FGD4
Hg19::chr12:32552770..32552839,+p4@FGD4
Hg19::chr12:32552842..32552853,+p13@FGD4
Hg19::chr12:32717031..32717041,+p@chr12:32717031..32717041
+
Hg19::chr12:32717043..32717051,+p@chr12:32717043..32717051
+
Hg19::chr12:47617402..47617434,+p8@FAM113B
Hg19::chr12:6309105..6309118,+p3@CD9
Hg19::chr12:76924954..76924956,-p@chr12:76924954..76924956
-
Hg19::chr12:7863680..7863695,+p3@DPPA3
Hg19::chr12:7864021..7864038,+p1@DPPA3
Hg19::chr12:7864063..7864074,+p2@DPPA3
Hg19::chr12:7868876..7868879,+p@chr12:7868876..7868879
+
Hg19::chr12:7949969..7949973,+p@chr12:7949969..7949973
+
Hg19::chr12:8983894..8983910,-p1@A2ML1-AS1
Hg19::chr14:53298995..53299003,+p@chr14:53298995..53299003
+
Hg19::chr14:55494125..55494134,-p3@WDHD1
Hg19::chr14:55494294..55494306,+p7@SOCS4
Hg19::chr14:55494309..55494321,+p8@SOCS4
Hg19::chr14:55494323..55494330,+p20@SOCS4
Hg19::chr14:65410551..65410554,-p@chr14:65410551..65410554
-
Hg19::chr14:65443815..65443820,-p@chr14:65443815..65443820
-
Hg19::chr14:89884879..89884907,-p@chr14:89884879..89884907
-
Hg19::chr15:85147079..85147099,+p4@ZSCAN2
Hg19::chr16:9069001..9069012,-p@chr16:9069001..9069012
-
Hg19::chr16:9069177..9069185,-p@chr16:9069177..9069185
-
Hg19::chr17:22021858..22021860,+p@chr17:22021858..22021860
+
Hg19::chr17:46608354..46608385,-p1@HOXB1
Hg19::chr18:19088172..19088187,+p@chr18:19088172..19088187
+
Hg19::chr19:37808831..37808843,+p6@HKR1
Hg19::chr19:408721..408732,-p1@AB384333
Hg19::chr19:41682068..41682081,-p@chr19:41682068..41682081
-
Hg19::chr19:42965112..42965160,+p@chr19:42965112..42965160
+
Hg19::chr19:49362621..49362640,-p6@PLEKHA4
Hg19::chr19:49362641..49362662,-p4@PLEKHA4
Hg19::chr19:53088167..53088194,+p@chr19:53088167..53088194
+
Hg19::chr1:111888934..111888946,+p4@C1orf88
Hg19::chr1:160924623..160924635,-p3@ITLN2
Hg19::chr1:235977099..235977107,-p@chr1:235977099..235977107
-
Hg19::chr1:247444566..247444577,+p@chr1:247444566..247444577
+
Hg19::chr1:27384953..27384985,+p@chr1:27384953..27384985
+
Hg19::chr1:28520384..28520393,-p15@PTAFR
Hg19::chr1:39696429..39696451,+p@chr1:39696429..39696451
+
Hg19::chr1:39696472..39696481,+p@chr1:39696472..39696481
+
Hg19::chr1:44584485..44584512,+p2@KLF17
Hg19::chr1:44584530..44584537,+p6@KLF17
Hg19::chr1:44584560..44584563,+p7@KLF17
Hg19::chr1:45769729..45769755,-p@chr1:45769729..45769755
-
Hg19::chr1:53308414..53308423,+p6@ZYG11A
Hg19::chr1:53308425..53308442,+p1@ZYG11A
Hg19::chr1:79959493..79959501,-p@chr1:79959493..79959501
-
Hg19::chr1:92406327..92406341,+p@chr1:92406327..92406341
+
Hg19::chr20:42295563..42295571,-p@chr20:42295563..42295571
-
Hg19::chr20:45948030..45948047,-p16@ZMYND8
Hg19::chr20:45948056..45948087,-p14@ZMYND8
Hg19::chr20:45948105..45948112,-p50@ZMYND8
Hg19::chr20:55200128..55200143,+p@chr20:55200128..55200143
+
Hg19::chr20:55205791..55205817,+p3@TFAP2C
Hg19::chr20:55205825..55205847,+p2@TFAP2C
Hg19::chr21:27478934..27478945,-p@chr21:27478934..27478945
-
Hg19::chr21:27478988..27478996,-p@chr21:27478988..27478996
-
Hg19::chr21:42617683..42617694,+p21@BACE2
Hg19::chr21:42617729..42617736,+p24@BACE2
Hg19::chr21:44345911..44345941,-p2@ERVH48-1
Hg19::chr21:45706354..45706368,+p@chr21:45706354..45706368
+
Hg19::chr22:31523734..31523780,+p3@INPP5J
Hg19::chr2:207068264..207068271,+p@chr2:207068264..207068271
+
Hg19::chr2:216410925..216410936,+p1@ENST00000417485
Hg19::chr2:230817260..230817303,+p@chr2:230817260..230817303
+
Hg19::chr2:230817333..230817366,+p@chr2:230817333..230817366
+
Hg19::chr2:233989536..233989550,+p@chr2:233989536..233989550
+
Hg19::chr2:233989556..233989568,+p@chr2:233989556..233989568
+
Hg19::chr2:3106559..3106568,-p@chr2:3106559..3106568
-
Hg19::chr2:65786044..65786055,+p@chr2:65786044..65786055
+
Hg19::chr2:71755206..71755213,+p@chr2:71755206..71755213
+
Hg19::chr2:71755221..71755234,+p@chr2:71755221..71755234
+
Hg19::chr2:71755236..71755242,+p@chr2:71755236..71755242
+
Hg19::chr3:185300270..185300303,+p5@SENP2
Hg19::chr3:185300305..185300324,+p7@SENP2
Hg19::chr3:185300358..185300377,+p6@SENP2
Hg19::chr3:185300391..185300410,+p10@SENP2
Hg19::chr3:47297118..47297149,+p@chr3:47297118..47297149
+
Hg19::chr3:99982282..99982305,+p@chr3:99982282..99982305
+
Hg19::chr4:165953213..165953229,+p2@TRIM60
Hg19::chr4:188915236..188915245,+p@chr4:188915236..188915245
+
Hg19::chr4:3931902..3931913,+p@chr4:3931902..3931913
+
Hg19::chr5:133764002..133764007,+p@chr5:133764002..133764007
+
Hg19::chr5:36596685..36596706,+p@chr5:36596685..36596706
+
Hg19::chr6:106909343..106909346,+p@chr6:106909343..106909346
+
Hg19::chr6:126066753..126066758,-p@chr6:126066753..126066758
-
Hg19::chr6:129812745..129812756,+p@chr6:129812745..129812756
+
Hg19::chr6:15022090..15022095,-p@chr6:15022090..15022095
-
Hg19::chr6:15022103..15022128,-p@chr6:15022103..15022128
-
Hg19::chr6:151773583..151773677,+p1@C6orf211
Hg19::chr6:31107482..31107498,-p2@PSORS1C2
Hg19::chr6:44106561..44106568,+p32@TMEM63B
Hg19::chr6:95268287..95268295,-p@chr6:95268287..95268295
-
Hg19::chr7:13699159..13699161,-p@chr7:13699159..13699161
-
Hg19::chr7:20874987..20875003,+p1@ENST00000447262
Hg19::chr7:20891733..20891735,+p@chr7:20891733..20891735
+
Hg19::chr7:63560612..63560634,+p1@GUSBP6
Hg19::chr8:136777354..136777357,+p@chr8:136777354..136777357
+
Hg19::chr8:59572532..59572546,-p26@NSMAF
Hg19::chr9:119600163..119600199,+p@chr9:119600163..119600199
+
Hg19::chr9:140560338..140560354,+p@chr9:140560338..140560354
+


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

No GOStat results

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
embryonic stem cell6.80e-825
germ line cell1.18e-387
germ cell1.18e-387
melanocyte1.65e-1510
melanoblast1.65e-1510
neuron8.35e-126
neuroblast8.35e-126
electrically signaling cell8.35e-126
pigment cell2.92e-1114
neuronal stem cell4.36e-098
neurecto-epithelial cell4.68e-0820
neurectodermal cell9.19e-0759
Uber Anatomy
Ontology termp-valuen
testis6.84e-348
male reproductive organ8.77e-2511
gonad3.61e-1321
indifferent external genitalia3.61e-1321
indifferent gonad3.61e-1321
gonad primordium3.61e-1321
external genitalia1.38e-1222
male organism1.38e-1222
male reproductive system1.38e-1222
Disease
Ontology termp-valuen
germ cell and embryonal cancer4.80e-1922
germ cell cancer4.80e-1922


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)
MA0003.10.526925
MA0004.10.00859436
MA0006.10.0374234
MA0007.10.0943663
MA0009.10.182343
MA0014.10.616642
MA0017.10.0753741
MA0019.10.248176
MA0024.10.76627
MA0025.10.0954284
MA0027.11.29955
MA0028.10.900608
MA0029.10.115979
MA0030.10.108329
MA0031.10.361737
MA0038.10.671671
MA0040.10.844169
MA0041.10.958006
MA0042.10.0210481
MA0043.10.409114
MA0046.10.0454027
MA0048.10.042861
MA0050.10.0213353
MA0051.10.0336052
MA0052.10.539094
MA0055.10.060453
MA0056.10
MA0057.10.129222
MA0058.10.00462671
MA0059.10.265465
MA0060.10.0062656
MA0061.10.441152
MA0063.10
MA0066.10.300874
MA0067.10.188442
MA0068.10.197509
MA0069.10.68359
MA0070.10.656034
MA0071.10.729411
MA0072.10.156854
MA0073.10.0275025
MA0074.10.083259
MA0076.10.449839
MA0077.10.347921
MA0078.10.550156
MA0081.10.175765
MA0083.10.739674
MA0084.10.311019
MA0087.11.41921
MA0088.12.18353
MA0089.10
MA0090.10.683714
MA0091.10.207512
MA0092.10.138684
MA0093.10.00320435
MA0095.10
MA0098.10
MA0100.10.509903
MA0101.10.190705
MA0103.10.706883
MA0105.11.49421
MA0106.10.0544844
MA0107.10.184336
MA0108.20.593644
MA0109.10
MA0111.10.761183
MA0113.10.660811
MA0114.10.0130228
MA0115.10.146118
MA0116.10.742614
MA0117.10.472556
MA0119.10.441463
MA0122.10.241804
MA0124.10.788795
MA0125.10.61709
MA0130.10
MA0131.10.102104
MA0132.10
MA0133.10
MA0135.10.798987
MA0136.10.0381595
MA0139.11.07496
MA0140.10.119229
MA0141.10.372477
MA0142.16.4743
MA0143.13.2712
MA0144.10.556579
MA0145.10.165173
MA0146.10.133145
MA0147.10.286862
MA0148.10.152823
MA0149.10.00479998
MA0062.20.315462
MA0035.20.213443
MA0039.21.42669
MA0138.20.553855
MA0002.20.00401526
MA0137.20.0296436
MA0104.20.670581
MA0047.20.220269
MA0112.20.0390175
MA0065.20.183472
MA0150.10.0460436
MA0151.10
MA0152.10.127147
MA0153.10.278214
MA0154.11.27942
MA0155.10.00506204
MA0156.10.102603
MA0157.10.124919
MA0158.10
MA0159.10.14563
MA0160.10.440647
MA0161.10
MA0162.10.401216
MA0163.10.577204
MA0164.10.70676
MA0080.20.0398065
MA0018.20.128567
MA0099.20.023276
MA0079.20.228222
MA0102.20.338081
MA0258.10.0684195
MA0259.10.041552
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
NANOG#79923142.924477848101270.0003393379346465960.0034498310675125
POU5F1#5460819.16795436868031.25431807001811e-089.32382383733958e-07



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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