Personal tools

Coexpression cluster:C189: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.061764068386534,0.0342676336102362,0.0329050193664387,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.910566711210503,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0473659963914933,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0413694521212564,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C189_b_splenic_tonsil_CD19_lymph_appendix_spleen
|full_id=C189_b_splenic_tonsil_CD19_lymph_appendix_spleen
|gostat_on_coexpression_clusters=GO:0009720!detection of hormone stimulus!0.0238912751849613!9619$GO:0019534!toxin transporter activity!0.0238912751849613!9619$GO:0015068!glycine amidinotransferase activity!0.0238912751849613!2628$GO:0015067!amidinotransferase activity!0.0238912751849613!2628$GO:0006600!creatine metabolic process!0.0238912751849613!2628$GO:0033700!phospholipid efflux!0.0238912751849613!9619$GO:0006601!creatine biosynthetic process!0.0238912751849613!2628$GO:0009726!detection of endogenous stimulus!0.0238912751849613!9619$GO:0055091!phospholipid homeostasis!0.0238912751849613!9619$GO:0006599!phosphagen metabolic process!0.0243383958235739!2628$GO:0042396!phosphagen biosynthetic process!0.0243383958235739!2628$GO:0051725!protein amino acid de-ADP-ribosylation!0.0243383958235739!141$GO:0003875!ADP-ribosylarginine hydrolase activity!0.0243383958235739!141$GO:0032365!intracellular lipid transport!0.0243383958235739!9619$GO:0032366!intracellular sterol transport!0.0243383958235739!9619$GO:0032367!intracellular cholesterol transport!0.0243383958235739!9619$GO:0008565!protein transporter activity!0.0243383958235739!5284;9619$GO:0005515!protein binding!0.0243383958235739!395;10095;285671;57596;5284;140691;3500;9045;9619$GO:0033344!cholesterol efflux!0.0339267824801768!9619$GO:0044446!intracellular organelle part!0.0341777671594579!395;10095;2628;140691;9045;9619$GO:0044422!organelle part!0.0341777671594579!395;10095;2628;140691;9045;9619$GO:0005885!Arp2/3 protein complex!0.0341777671594579!10095$GO:0042987!amyloid precursor protein catabolic process!0.0373554338073769!9619$GO:0043531!ADP binding!0.0402667158160958!9619$GO:0017127!cholesterol transporter activity!0.0472295975431517!9619
|gostat_on_coexpression_clusters=GO:0009720!detection of hormone stimulus!0.0238912751849613!9619$GO:0019534!toxin transporter activity!0.0238912751849613!9619$GO:0015068!glycine amidinotransferase activity!0.0238912751849613!2628$GO:0015067!amidinotransferase activity!0.0238912751849613!2628$GO:0006600!creatine metabolic process!0.0238912751849613!2628$GO:0033700!phospholipid efflux!0.0238912751849613!9619$GO:0006601!creatine biosynthetic process!0.0238912751849613!2628$GO:0009726!detection of endogenous stimulus!0.0238912751849613!9619$GO:0055091!phospholipid homeostasis!0.0238912751849613!9619$GO:0006599!phosphagen metabolic process!0.0243383958235739!2628$GO:0042396!phosphagen biosynthetic process!0.0243383958235739!2628$GO:0051725!protein amino acid de-ADP-ribosylation!0.0243383958235739!141$GO:0003875!ADP-ribosylarginine hydrolase activity!0.0243383958235739!141$GO:0032365!intracellular lipid transport!0.0243383958235739!9619$GO:0032366!intracellular sterol transport!0.0243383958235739!9619$GO:0032367!intracellular cholesterol transport!0.0243383958235739!9619$GO:0008565!protein transporter activity!0.0243383958235739!5284;9619$GO:0005515!protein binding!0.0243383958235739!395;10095;285671;57596;5284;140691;3500;9045;9619$GO:0033344!cholesterol efflux!0.0339267824801768!9619$GO:0044446!intracellular organelle part!0.0341777671594579!395;10095;2628;140691;9045;9619$GO:0044422!organelle part!0.0341777671594579!395;10095;2628;140691;9045;9619$GO:0005885!Arp2/3 protein complex!0.0341777671594579!10095$GO:0042987!amyloid precursor protein catabolic process!0.0373554338073769!9619$GO:0043531!ADP binding!0.0402667158160958!9619$GO:0017127!cholesterol transporter activity!0.0472295975431517!9619

Revision as of 14:31, 12 September 2012


Full id: C189_b_splenic_tonsil_CD19_lymph_appendix_spleen



Phase1 CAGE Peaks

Hg19::chr10:267221..267230,+p@chr10:267221..267230
+
Hg19::chr10:37455757..37455787,+p@chr10:37455757..37455787
+
Hg19::chr10:79970622..79970624,+p@chr10:79970622..79970624
+
Hg19::chr12:123416933..123416944,-p@chr12:123416933..123416944
-
Hg19::chr12:68835921..68835926,-p2@ENST00000546086
Hg19::chr13:100375524..100375531,+p@chr13:100375524..100375531
+
Hg19::chr13:100377188..100377194,+p@chr13:100377188..100377194
+
Hg19::chr13:100377368..100377389,+p@chr13:100377368..100377389
+
Hg19::chr14:101036119..101036130,-p20@BEGAIN
Hg19::chr14:106161355..106161362,-p@chr14:106161355..106161362
-
Hg19::chr14:106327961..106327980,-p2@DQ431661
Hg19::chr14:106351913..106351948,-p1@IGHD3-22
Hg19::chr14:106877761..106877767,-p1@AF460681
p1@AF460715
p1@AF460721
p1@AF460739
p1@AF460749
p1@AF460752
p1@AF460755
p1@AF460757
p1@AF460765
p1@AF460795
p1@AF460799
p1@AF460809
p1@AF460810
p1@AF460812
p1@AF460813
p1@AF460814
p1@AF460816
p1@AF460819
p1@AF460820
p1@AF460831
p1@AF460842
Hg19::chr14:106878083..106878099,-p1@IGHV4-39
Hg19::chr14:75981521..75981530,+p@chr14:75981521..75981530
+
Hg19::chr15:45028719..45028738,+p6@TRIM69
Hg19::chr15:45671019..45671033,-p7@GATM
Hg19::chr15:52404161..52404166,+p@chr15:52404161..52404166
+
Hg19::chr15:52404181..52404187,+p@chr15:52404181..52404187
+
Hg19::chr15:57506462..57506496,+p36@TCF12
Hg19::chr15:78177670..78177678,+p@chr15:78177670..78177678
+
Hg19::chr16:4975293..4975294,+p@chr16:4975293..4975294
+
Hg19::chr16:53412335..53412342,+p@chr16:53412335..53412342
+
Hg19::chr16:53412381..53412387,+p@chr16:53412381..53412387
+
Hg19::chr16:76613424..76613434,+p@chr16:76613424..76613434
+
Hg19::chr16:76613646..76613671,+p@chr16:76613646..76613671
+
Hg19::chr17:48994960..48994968,+p@chr17:48994960..48994968
+
Hg19::chr17:55334804..55334824,+p@chr17:55334804..55334824
+
Hg19::chr17:70420105..70420110,+p@chr17:70420105..70420110
+
Hg19::chr17:70420494..70420517,+p@chr17:70420494..70420517
+
Hg19::chr17:78371475..78371480,+p@chr17:78371475..78371480
+
Hg19::chr17:80328570..80328583,+p@chr17:80328570..80328583
+
Hg19::chr17:80328744..80328754,+p@chr17:80328744..80328754
+
Hg19::chr18:74240756..74240772,+p2@LOC284276
Hg19::chr1:173379658..173379666,-p@chr1:173379658..173379666
-
Hg19::chr1:207105167..207105184,-p5@PIGR
Hg19::chr1:207105188..207105210,-p3@PIGR
Hg19::chr1:207105216..207105252,-p4@PIGR
Hg19::chr1:22502943..22502969,+p@chr1:22502943..22502969
+
Hg19::chr1:25799245..25799271,+p@chr1:25799245..25799271
+
Hg19::chr1:31896395..31896404,+p@chr1:31896395..31896404
+
Hg19::chr1:31896446..31896458,+p@chr1:31896446..31896458
+
Hg19::chr21:43704482..43704491,+p9@ABCG1
Hg19::chr21:43706764..43706775,+p@chr21:43706764..43706775
+
Hg19::chr22:22930643..22930649,+p1@IGLV2-33
Hg19::chr22:23040132..23040138,+p1@IGLV2-23
Hg19::chr22:23040389..23040405,+p1@ENST00000385095
Hg19::chr22:23040696..23040701,+p1@AJ408281
Hg19::chr22:34616800..34616810,+p@chr22:34616800..34616810
+
Hg19::chr22:34653635..34653640,+p@chr22:34653635..34653640
+
Hg19::chr22:37484895..37484906,-p@chr22:37484895..37484906
-
Hg19::chr22:37484928..37484953,-p@chr22:37484928..37484953
-
Hg19::chr2:111538269..111538279,+p@chr2:111538269..111538279
+
Hg19::chr2:160779191..160779202,-p@chr2:160779191..160779202
-
Hg19::chr2:170998413..170998419,-p@chr2:170998413..170998419
-
Hg19::chr2:170998667..170998714,+p@chr2:170998667..170998714
+
Hg19::chr2:54810455..54810472,-p@chr2:54810455..54810472
-
Hg19::chr3:108014582..108014611,+p@chr3:108014582..108014611
+
Hg19::chr3:118484990..118484992,-p@chr3:118484990..118484992
-
Hg19::chr3:119299336..119299359,+p12@ADPRH
Hg19::chr3:166801172..166801180,-p@chr3:166801172..166801180
-
Hg19::chr3:171076173..171076182,-p@chr3:171076173..171076182
-
Hg19::chr3:31431437..31431441,+p@chr3:31431437..31431441
+
Hg19::chr3:61896640..61896646,+p@chr3:61896640..61896646
+
Hg19::chr3:96533659..96533667,+p11@EPHA6
Hg19::chr3:96533671..96533680,+p10@EPHA6
Hg19::chr3:96533682..96533687,+p13@EPHA6
Hg19::chr5:169494477..169494513,+p@chr5:169494477..169494513
+
Hg19::chr5:26877471..26877484,+p@chr5:26877471..26877484
+
Hg19::chr5:26877490..26877500,+p@chr5:26877490..26877500
+
Hg19::chr5:26877504..26877517,+p@chr5:26877504..26877517
+
Hg19::chr5:26877541..26877549,+p@chr5:26877541..26877549
+
Hg19::chr5:63461151..63461183,+p4@RNF180
Hg19::chr5:63461191..63461205,+p5@RNF180
Hg19::chr5:80255013..80255020,+p@chr5:80255013..80255020
+
Hg19::chr6:113971101..113971111,-p@chr6:113971101..113971111
-
Hg19::chr6:113971125..113971136,-p@chr6:113971125..113971136
-
Hg19::chr6:149353791..149353807,-p3@ENST00000433442
Hg19::chr6:149353870..149353873,-p8@ENST00000433442
Hg19::chr7:30803690..30803693,-p@chr7:30803690..30803693
-
Hg19::chr8:72753886..72753911,+p@chr8:72753886..72753911
+
Hg19::chr8:87719795..87719814,+p1@ENST00000519041
Hg19::chr8:87719833..87719844,+p2@ENST00000519041
Hg19::chr9:128397835..128397850,-p@chr9:128397835..128397850
-
Hg19::chr9:5580708..5580720,-p@chr9:5580708..5580720
-
Hg19::chrX:114701086..114701089,+p@chrX:114701086..114701089
+
Hg19::chrX:11682523..11682558,-p26@ARHGAP6
Hg19::chrX:48792308..48792316,-p20@OTUD5
Hg19::chrX:48792324..48792350,-p14@OTUD5


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:0009720detection of hormone stimulus0.0238912751849613
GO:0019534toxin transporter activity0.0238912751849613
GO:0015068glycine amidinotransferase activity0.0238912751849613
GO:0015067amidinotransferase activity0.0238912751849613
GO:0006600creatine metabolic process0.0238912751849613
GO:0033700phospholipid efflux0.0238912751849613
GO:0006601creatine biosynthetic process0.0238912751849613
GO:0009726detection of endogenous stimulus0.0238912751849613
GO:0055091phospholipid homeostasis0.0238912751849613
GO:0006599phosphagen metabolic process0.0243383958235739
GO:0042396phosphagen biosynthetic process0.0243383958235739
GO:0051725protein amino acid de-ADP-ribosylation0.0243383958235739
GO:0003875ADP-ribosylarginine hydrolase activity0.0243383958235739
GO:0032365intracellular lipid transport0.0243383958235739
GO:0032366intracellular sterol transport0.0243383958235739
GO:0032367intracellular cholesterol transport0.0243383958235739
GO:0008565protein transporter activity0.0243383958235739
GO:0005515protein binding0.0243383958235739
GO:0033344cholesterol efflux0.0339267824801768
GO:0044446intracellular organelle part0.0341777671594579
GO:0044422organelle part0.0341777671594579
GO:0005885Arp2/3 protein complex0.0341777671594579
GO:0042987amyloid precursor protein catabolic process0.0373554338073769
GO:0043531ADP binding0.0402667158160958
GO:0017127cholesterol transporter activity0.0472295975431517



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><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.91e-33115
blood3.56e-0915
haemolymphatic fluid3.56e-0915
organism substance3.56e-0915
hematopoietic system4.01e-08102
blood island4.01e-08102
central nervous system6.45e-0882
neural tube7.77e-0857
neural rod7.77e-0857
future spinal cord7.77e-0857
neural keel7.77e-0857
anterior neural tube3.45e-0742
hemolymphoid system7.97e-07112
regional part of forebrain8.67e-0741
forebrain8.67e-0741
future forebrain8.67e-0741


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
BATF#10538102.736831662056590.003574132678959090.0181062690559667
EBF1#1879202.001453223948090.001804936358579670.010918375230449



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:C189&oldid=2136515"