Personal tools

Coexpression cluster:C478

From FANTOM5_SSTAR

Revision as of 14:15, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C478_blood_Whole_Reticulocytes_liver_skeletal_lung_Neutrophils



Phase1 CAGE Peaks

Hg19::chr11:5247855..5247868,+p1@DQ655984
Hg19::chr11:5247857..5247902,-p2@HBB
Hg19::chr11:5247918..5247954,-p5@HBB
Hg19::chr12:10875643..10875687,+p@chr12:10875643..10875687
+
Hg19::chr12:25204833..25204837,+p26@LRMP
Hg19::chr15:77973117..77973119,+p@chr15:77973117..77973119
+
Hg19::chr16:223575..223610,+p@chr16:223575..223610
+
Hg19::chr16:223611..223622,+p@chr16:223611..223622
+
Hg19::chr17:47302378..47302387,-p@chr17:47302378..47302387
-
Hg19::chr19:7755354..7755360,-p@chr19:7755354..7755360
-
Hg19::chr1:172425609..172425633,-p@chr1:172425609..172425633
-
Hg19::chr1:28906381..28906392,-p3@SNORA61
Hg19::chr21:35902242..35902243,+p@chr21:35902242..35902243
+
Hg19::chr5:86705141..86705152,-p@chr5:86705141..86705152
-
Hg19::chr7:141998622..141998625,+p7@TRBV1
Hg19::chr7:150233619..150233622,+p@chr7:150233619..150233622
+
Hg19::chr8:21924232..21924243,+p27@EPB49
Hg19::chr9:21031599..21031600,-p3@PTPLAD2
Hg19::chr9:77567516..77567525,-p10@C9orf40
Hg19::chrX:133894375..133894379,-p1@ENST00000363050


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:0006906vesicle fusion0.0169630723455826
GO:0007516hemocyte development0.0169630723455826
GO:0042386hemocyte differentiation0.0169630723455826
GO:0006903vesicle targeting0.0169630723455826
GO:0051650establishment of vesicle localization0.0169630723455826
GO:0051648vesicle localization0.0169630723455826
GO:0007010cytoskeleton organization and biogenesis0.0169630723455826
GO:0051017actin filament bundle formation0.0169630723455826
GO:0051693actin filament capping0.0169630723455826
GO:0051016barbed-end actin filament capping0.0169630723455826
GO:0030835negative regulation of actin filament depolymerization0.0169630723455826
GO:0030834regulation of actin filament depolymerization0.0169630723455826
GO:0030042actin filament depolymerization0.0169630723455826
GO:0051656establishment of organelle localization0.0169630723455826
GO:0005344oxygen transporter activity0.0179282200907595
GO:0005833hemoglobin complex0.0179282200907595
GO:0015671oxygen transport0.0179282200907595
GO:0015669gas transport0.0179282200907595
GO:0051640organelle localization0.0179282200907595
GO:0006944membrane fusion0.0186518664011759
GO:0007015actin filament organization0.0186518664011759
GO:0008064regulation of actin polymerization and/or depolymerization0.0186518664011759
GO:0051261protein depolymerization0.0186518664011759
GO:0030832regulation of actin filament length0.0186518664011759
GO:0032535regulation of cellular component size0.0186518664011759
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0186518664011759
GO:0051129negative regulation of cellular component organization and biogenesis0.0195985291444856
GO:0051493regulation of cytoskeleton organization and biogenesis0.0195985291444856
GO:0033043regulation of organelle organization and biogenesis0.0195985291444856
GO:0019825oxygen binding0.0195985291444856
GO:0008154actin polymerization and/or depolymerization0.0202948970506126
GO:0006996organelle organization and biogenesis0.0214567854777106
GO:0051128regulation of cellular component organization and biogenesis0.0312180513871598
GO:0051248negative regulation of protein metabolic process0.0315081544032493
GO:0005737cytoplasm0.0357002929817791
GO:0030097hemopoiesis0.0459898790239126
GO:0048534hemopoietic or lymphoid organ development0.0480650732299859
GO:0002520immune system development0.0492218306408048



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
blood1.48e-4915
haemolymphatic fluid1.48e-4915
organism substance1.48e-4915
adult organism2.02e-18114
lower lobe of right lung6.82e-131
right lung lobe6.82e-131
lower lobe of lung6.82e-131
lobe of lung6.82e-131
right lung6.82e-131
dura mater9.73e-131
future meninx9.73e-131
ectomeninx9.73e-131
future dura mater9.73e-131
hematopoietic system1.24e-1098
blood island1.24e-1098
hemolymphoid system1.54e-09108
hemopoietic organ1.68e-077
immune organ1.68e-077
meninx5.28e-072
membrane organ5.28e-072
meningeal cluster5.28e-072


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

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C478&oldid=2556812"