Personal tools

Coexpression cluster:C186

From FANTOM5_SSTAR

Revision as of 14:16, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C186_squamous_papillotubular_large_Tracheal_oral_Small_epidermoid



Phase1 CAGE Peaks

Hg19::chr11:119461966..119461970,+p@chr11:119461966..119461970
+
Hg19::chr11:12211354..12211375,+p@chr11:12211354..12211375
+
Hg19::chr11:12211377..12211384,+p@chr11:12211377..12211384
+
Hg19::chr11:12211454..12211464,+p@chr11:12211454..12211464
+
Hg19::chr11:12211480..12211490,+p@chr11:12211480..12211490
+
Hg19::chr11:393795..393799,-p@chr11:393795..393799
-
Hg19::chr11:64774309..64774333,-p@chr11:64774309..64774333
-
Hg19::chr11:64774372..64774383,-p@chr11:64774372..64774383
-
Hg19::chr11:64774464..64774480,-p@chr11:64774464..64774480
-
Hg19::chr11:65683410..65683420,+p@chr11:65683410..65683420
+
Hg19::chr11:65683428..65683475,+p@chr11:65683428..65683475
+
Hg19::chr11:90222429..90222464,+p@chr11:90222429..90222464
+
Hg19::chr12:65362955..65362961,-p@chr12:65362955..65362961
-
Hg19::chr12:66049021..66049034,-p@chr12:66049021..66049034
-
Hg19::chr12:72104152..72104171,-p1@ENST00000549710
Hg19::chr12:76228513..76228524,-p@chr12:76228513..76228524
-
Hg19::chr12:76228543..76228556,-p@chr12:76228543..76228556
-
Hg19::chr13:74071833..74071844,+p@chr13:74071833..74071844
+
Hg19::chr13:74071854..74071871,+p@chr13:74071854..74071871
+
Hg19::chr13:74071880..74071894,+p@chr13:74071880..74071894
+
Hg19::chr14:29593762..29593772,-p@chr14:29593762..29593772
-
Hg19::chr14:47683291..47683294,-p@chr14:47683291..47683294
-
Hg19::chr14:70466297..70466304,+p@chr14:70466297..70466304
+
Hg19::chr14:71275492..71275543,+p@chr14:71275492..71275543
+
Hg19::chr14:71276610..71276625,+p2@ENST00000554032
Hg19::chr14:71276645..71276721,+p1@ENST00000554032
Hg19::chr15:101417937..101417955,+p8@ALDH1A3
Hg19::chr15:101417973..101417981,+p10@ALDH1A3
Hg19::chr15:101418003..101418019,+p5@ALDH1A3
Hg19::chr15:71389281..71389306,+p4@THSD4
Hg19::chr16:70838983..70838988,-p@chr16:70838983..70838988
-
Hg19::chr16:82671393..82671425,+p@chr16:82671393..82671425
+
Hg19::chr16:82671490..82671521,+p@chr16:82671490..82671521
+
Hg19::chr17:30487950..30487952,-p@chr17:30487950..30487952
-
Hg19::chr17:76506753..76506758,-p11@DNAH17
Hg19::chr19:3656823..3656835,-p@chr19:3656823..3656835
-
Hg19::chr19:39574692..39574701,-p@chr19:39574692..39574701
-
Hg19::chr1:158116675..158116685,-p@chr1:158116675..158116685
-
Hg19::chr1:247692872..247692880,+p@chr1:247692872..247692880
+
Hg19::chr1:55436540..55436544,-p@chr1:55436540..55436544
-
Hg19::chr1:58310606..58310611,-p@chr1:58310606..58310611
-
Hg19::chr20:1459305..1459323,-p@chr20:1459305..1459323
-
Hg19::chr20:49948180..49948199,-p@chr20:49948180..49948199
-
Hg19::chr20:50253078..50253081,+p@chr20:50253078..50253081
+
Hg19::chr3:133199287..133199293,-p@chr3:133199287..133199293
-
Hg19::chr3:162157693..162157708,-p@chr3:162157693..162157708
-
Hg19::chr3:184050382..184050388,+p@chr3:184050382..184050388
+
Hg19::chr3:83227676..83227682,-p@chr3:83227676..83227682
-
Hg19::chr3:8721551..8721586,-p@chr3:8721551..8721586
-
Hg19::chr4:137842587..137842589,-p1@ENST00000512039
Hg19::chr4:149677484..149677487,-p@chr4:149677484..149677487
-
Hg19::chr4:165056668..165056683,-p15@MARCH1
Hg19::chr4:22999152..22999159,+p1@ENST00000511453
p1@uc003gqr.1
Hg19::chr4:75410084..75410098,+p@chr4:75410084..75410098
+
Hg19::chr5:167182003..167182007,-p@chr5:167182003..167182007
-
Hg19::chr5:72598821..72598846,+p@chr5:72598821..72598846
+
Hg19::chr5:72708695..72708700,+p@chr5:72708695..72708700
+
Hg19::chr5:72708745..72708758,+p@chr5:72708745..72708758
+
Hg19::chr5:86415919..86415926,+p1@ENST00000515750
p1@uc003kit.2
Hg19::chr5:8981522..8981557,+p@chr5:8981522..8981557
+
Hg19::chr5:8984611..8984621,-p@chr5:8984611..8984621
-
Hg19::chr5:95404206..95404210,-p@chr5:95404206..95404210
-
Hg19::chr6:143654483..143654535,+p@chr6:143654483..143654535
+
Hg19::chr6:70320255..70320261,-p@chr6:70320255..70320261
-
Hg19::chr7:48075159..48075177,+p2@C7orf57
Hg19::chr7:55775905..55775916,-p@chr7:55775905..55775916
-
Hg19::chr7:64300314..64300319,-p@chr7:64300314..64300319
-
Hg19::chr7:75715539..75715572,-p@chr7:75715539..75715572
-
Hg19::chr7:98805698..98805708,-p@chr7:98805698..98805708
-
Hg19::chr7:98805731..98805743,-p@chr7:98805731..98805743
-
Hg19::chr7:98870435..98870449,+p6@MYH16
Hg19::chr7:98870454..98870479,+p1@MYH16
Hg19::chr7:98870482..98870519,+p2@MYH16
Hg19::chr7:98870526..98870537,+p5@MYH16
Hg19::chr7:98870790..98870795,+p7@MYH16
Hg19::chr7:98870934..98870947,+p4@MYH16
Hg19::chr7:98870948..98870967,+p3@MYH16
Hg19::chr7:98870980..98870981,+p8@MYH16
Hg19::chr8:117456880..117456884,-p@chr8:117456880..117456884
-
Hg19::chr8:123102017..123102025,-p@chr8:123102017..123102025
-
Hg19::chr8:123139536..123139544,-p1@ENST00000523792
p1@uc003ypj.2
Hg19::chr8:126044339..126044344,-p@chr8:126044339..126044344
-
Hg19::chr8:127596030..127596033,+p@chr8:127596030..127596033
+
Hg19::chr8:76774227..76774234,+p@chr8:76774227..76774234
+
Hg19::chr8:87834707..87834714,+p@chr8:87834707..87834714
+
Hg19::chr8:90624105..90624144,-p@chr8:90624105..90624144
-
Hg19::chr9:124328237..124328240,+p@chr9:124328237..124328240
+
Hg19::chrX:19692351..19692356,-p@chrX:19692351..19692356
-
Hg19::chrX:25540398..25540420,+p@chrX:25540398..25540420
+
Hg19::chrX:25540422..25540429,+p@chrX:25540422..25540429
+
Hg19::chrX:29431271..29431280,+p@chrX:29431271..29431280
+
Hg19::chrX:35470106..35470112,+p@chrX:35470106..35470112
+


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:0060166olfactory pit development0.00603402598852654
GO:0002072optic cup morphogenesis involved in camera-type eye development0.00603402598852654
GO:0021768nucleus accumbens development0.00603402598852654
GO:0043584nose development0.00603402598852654
GO:0021756striatum development0.00603402598852654
GO:0048857neural nucleus development0.00603402598852654
GO:0021544subpallium development0.00775757666933773
GO:0048048embryonic eye morphogenesis0.00904997327703826
GO:0042573retinoic acid metabolic process0.0100549338569124
GO:00040283-chloroallyl aldehyde dehydrogenase activity0.0108586892361296
GO:0021761limbic system development0.0115161135774329
GO:0048562embryonic organ morphogenesis0.0150779615211111
GO:0021537telencephalon development0.0153090288070116
GO:0048593camera-type eye morphogenesis0.0167981898572595
GO:0004030aldehyde dehydrogenase [NAD(P)+] activity0.016883340376704
GO:0006776vitamin A metabolic process0.0169577140091317
GO:0006775fat-soluble vitamin metabolic process0.0191488592113784
GO:0048568embryonic organ development0.0200921158836862
GO:0016331morphogenesis of embryonic epithelium0.0209356343747139
GO:0048592eye morphogenesis0.0234994728631865
GO:0043010camera-type eye development0.0292529612633874
GO:0030286dynein complex0.0339912580765414
GO:0030900forebrain development0.0339912580765414
GO:0001654eye development0.0339912580765414
GO:0044430cytoskeletal part0.0339912580765414
GO:0016620oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor0.0347134486806925
GO:0002009morphogenesis of an epithelium0.0420867596980804
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0463567570676262



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
ectoderm-derived structure6.47e-09169
ectoderm9.30e-09173
presumptive ectoderm9.30e-09173
endoderm-derived structure1.55e-08169
endoderm1.55e-08169
presumptive endoderm1.55e-08169
organ part5.77e-08219
anatomical space6.87e-08104
respiratory tract epithelium3.33e-0719
lung epithelium3.33e-0719
respiratory system5.42e-0772
female organism5.54e-0741
organism subdivision6.23e-07365
Disease
Ontology termp-valuen
disease of cellular proliferation4.34e-32239
cell type cancer8.35e-31143
cancer8.61e-31235
carcinoma5.13e-29106
organ system cancer7.57e-12137
adenocarcinoma1.28e-1025
squamous cell carcinoma1.12e-0914
disease of anatomical entity6.93e-0739


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:C186&oldid=1704549"