Personal tools

Coexpression cluster:C128: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C128_testicular_choriocarcinoma_H9_teratocarcinoma_pancreatic_iPS_HES3GFP |id=C128 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C128_testicular_choriocarcinoma_H9_teratocarcinoma_pancreatic_iPS_HES3GFP
|full_id=C128_testicular_choriocarcinoma_H9_teratocarcinoma_pancreatic_iPS_HES3GFP
|id=C128
|id=C128
|ontology_enrichment_celltype=CL:0000066!1.79e-10!254;CL:0002139!1.06e-09!24;CL:0000115!4.46e-07!35;CL:0000071!5.05e-07!18;CL:0002546!5.05e-07!18
|ontology_enrichment_disease=DOID:305!4.37e-10!106;DOID:0050687!6.34e-09!143
|ontology_enrichment_uberon=UBERON:0005743!1.99e-22!86;UBERON:0000073!5.50e-22!94;UBERON:0001016!5.50e-22!94;UBERON:0001017!1.52e-21!82;UBERON:0001049!2.45e-20!57;UBERON:0005068!2.45e-20!57;UBERON:0006241!2.45e-20!57;UBERON:0007135!2.45e-20!57;UBERON:0003075!2.07e-17!86;UBERON:0007284!2.07e-17!86;UBERON:0004121!3.65e-17!169;UBERON:0000924!1.33e-16!173;UBERON:0006601!1.33e-16!173;UBERON:0002780!1.64e-16!41;UBERON:0001890!1.64e-16!41;UBERON:0006240!1.64e-16!41;UBERON:0002616!1.93e-16!59;UBERON:0002346!2.06e-16!90;UBERON:0003080!2.09e-16!42;UBERON:0000955!5.66e-16!69;UBERON:0006238!5.66e-16!69;UBERON:0000062!1.83e-15!511;UBERON:0002020!2.57e-15!34;UBERON:0003528!2.57e-15!34;UBERON:0001893!4.21e-15!34;UBERON:0002791!1.37e-14!33;UBERON:0001869!1.45e-14!32;UBERON:0000468!1.65e-14!659;UBERON:0000480!2.03e-14!626;UBERON:0000033!2.49e-14!123;UBERON:0003056!3.48e-14!61;UBERON:0000467!3.57e-14!625;UBERON:0000153!6.69e-14!129;UBERON:0007811!6.69e-14!129;UBERON:0000922!4.61e-12!612;UBERON:0000956!5.25e-12!25;UBERON:0000203!5.25e-12!25;UBERON:0007023!1.36e-11!115;UBERON:0002619!2.45e-10!22;UBERON:0002050!9.94e-10!605;UBERON:0005423!9.94e-10!605;UBERON:0001950!1.01e-09!20;UBERON:0000923!2.12e-09!604;UBERON:0005291!2.12e-09!604;UBERON:0006598!2.12e-09!604;UBERON:0002532!2.12e-09!604;UBERON:0000064!2.98e-09!219;UBERON:0001986!5.05e-07!18;UBERON:0004638!5.05e-07!18;UBERON:0004852!5.05e-07!18
}}
}}

Revision as of 14:09, 21 May 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>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system5.50e-2294
nervous system5.50e-2294
central nervous system1.52e-2182
neural tube2.45e-2057
neural rod2.45e-2057
future spinal cord2.45e-2057
neural keel2.45e-2057
neural plate2.07e-1786
presumptive neural plate2.07e-1786
ectoderm-derived structure3.65e-17169
ectoderm1.33e-16173
presumptive ectoderm1.33e-16173
regional part of forebrain1.64e-1641
forebrain1.64e-1641
future forebrain1.64e-1641
regional part of brain1.93e-1659
neurectoderm2.06e-1690
anterior neural tube2.09e-1642
brain5.66e-1669
future brain5.66e-1669
organ1.83e-15511
gray matter2.57e-1534
brain grey matter2.57e-1534
telencephalon4.21e-1534
regional part of telencephalon1.37e-1433
cerebral hemisphere1.45e-1432
multi-cellular organism1.65e-14659
anatomical group2.03e-14626
head2.49e-14123
pre-chordal neural plate3.48e-1461
anatomical system3.57e-14625
anterior region of body6.69e-14129
craniocervical region6.69e-14129
embryo4.61e-12612
cerebral cortex5.25e-1225
pallium5.25e-1225
adult organism1.36e-11115
regional part of cerebral cortex2.45e-1022
embryonic structure9.94e-10605
developing anatomical structure9.94e-10605
neocortex1.01e-0920
germ layer2.12e-09604
embryonic tissue2.12e-09604
presumptive structure2.12e-09604
epiblast (generic)2.12e-09604
organ part2.98e-09219
endothelium5.05e-0718
blood vessel endothelium5.05e-0718
cardiovascular system endothelium5.05e-0718
Disease
Ontology termp-valuen
carcinoma4.37e-10106
cell type cancer6.34e-09143


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

No analysis results for this cluster

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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C128&oldid=1703905"