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Coexpression cluster:C128: Difference between revisions

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|tf_chipseq_enrich=NANOG#79923;14:2.92447784810127:0.000339337934646596:0.0034498310675125!POU5F1#5460;8:19.1679543686803:1.25431807001811e-08:9.32382383733958e-07
|tf_chipseq_enrich=NANOG#79923;14:2.92447784810127:0.000339337934646596:0.0034498310675125!POU5F1#5460;8:19.1679543686803:1.25431807001811e-08:9.32382383733958e-07
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|tfbs_overrepresentation_for_novel_motifs=0.975145,1.25072,0.56552,0.0369372,0.019297,1.5533,0.902143,0.275125,0.262928,0.104274,1.05245,0.239258,1.75328,0.615562,0.0377648,0.463508,0.0801398,0.845764,0.52094,0.10965,0.134508,1.09083,0.528848,1.3431,0.484648,1.59849,2.12764,0.0720137,0.186754,0.801404,0.152586,0.101624,0.574191,0.537792,0.423729,0.031955,0.407033,0.767221,0.0357289,0.518277,0.311039,0.317713,2.39758,0.00783634,0.329655,0.0707326,0.0860099,0.406224,0.122153,0.271342,0.168315,0.0961918,0.614724,0.358553,0.0900075,0.860106,0.130076,0.943572,0.67981,0.938062,0.129099,1.20107,0.0969629,0.173625,1.01069,0.0506555,0.405818,0.362748,0.448437,0.692965,0.40416,0.753523,0.410595,0.62252,0.176498,0.679286,0.0407154,0.531068,0.232415,0.220547,0.963033,0.0138287,0.103678,0.155869,0.0698604,0.470267,0.0175692,0.0884043,0.0317381,0.440064,0.178921,0.477566,0.271871,1.5099,0.18063,0.0540123,1.03525,0.601862,0.20894,0.449169,0.00956158,0.108732,0.138491,0.981196,0.458568,1.27876,0.0736993,0.149439,0.346547,1.69009,0.344929,0.319937,0.285982,0.210638,0.464129,0.398902,0.547546,0.150573,0.0497081,0.109925,0.606501,1.47113,0.548592,0.0482885,0.216206,0.314943,1.14264,1.62489,0.690606,1.0847,0.219922,1.17031,0.355138,0.013937,0.547061,0.296889,1.10581,1.47747,0.162438,0.837734,0.482615,0.142697,0.0324215,0.140024,0.712422,0.107141,0.115484,0.692378,0.3077,0.144744,0.249354,0.595145,0.479441,0.165731,0.0353362,0.268445,0.328066,0.0542735,0.045677,0.255769,0.142075,0.447505,0.231435,0.265263,0.0532764,0.200834,0.780206,0.65527,0.00246201
}}
}}

Revision as of 13:31, 26 November 2012


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)

{{{tfbs_overrepresentation_jaspar}}}



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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