Personal tools

Coexpression cluster:C686: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C686_CD14_immature_CD19_Eosinophils_migratory_Mast_Basophils |id=C686 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C686_CD14_immature_CD19_Eosinophils_migratory_Mast_Basophils
|full_id=C686_CD14_immature_CD19_Eosinophils_migratory_Mast_Basophils
|gostat_on_coexpression_clusters=GO:0016973!poly(A)+ mRNA export from nucleus!0.00794725374557758!10482$GO:0050858!negative regulation of antigen receptor-mediated signaling pathway!0.00794725374557758!1997$GO:0050860!negative regulation of T cell receptor signaling pathway!0.00794725374557758!1997$GO:0042405!nuclear inclusion body!0.00794725374557758!10482$GO:0016234!inclusion body!0.0105950906474368!10482$GO:0050856!regulation of T cell receptor signaling pathway!0.0105950906474368!1997$GO:0005487!nucleocytoplasmic transporter activity!0.0105950906474368!10482$GO:0050854!regulation of antigen receptor-mediated signaling pathway!0.0132426936896461!1997$GO:0050852!T cell receptor signaling pathway!0.0200070579879434!1997$GO:0006406!mRNA export from nucleus!0.0211733427389052!10482$GO:0050851!antigen receptor-mediated signaling pathway!0.0211733427389052!1997$GO:0002429!immune response-activating cell surface receptor signaling pathway!0.0211733427389052!1997$GO:0006405!RNA export from nucleus!0.0211733427389052!10482$GO:0002768!immune response-regulating cell surface receptor signaling pathway!0.0211733427389052!1997$GO:0002757!immune response-activating signal transduction!0.0211733427389052!1997$GO:0002764!immune response-regulating signal transduction!0.0211733427389052!1997$GO:0003729!mRNA binding!0.0211733427389052!10482$GO:0006955!immune response!0.0228402138005044!1997;9308$GO:0001817!regulation of cytokine production!0.0228402138005044!1997$GO:0051168!nuclear export!0.0232838193519774!10482$GO:0002376!immune system process!0.027740075393911!1997;9308$GO:0002253!activation of immune response!0.0308132798303632!1997$GO:0006959!humoral immune response!0.0308132798303632!9308$GO:0051028!mRNA transport!0.0308132798303632!10482$GO:0050778!positive regulation of immune response!0.0308132798303632!1997$GO:0002684!positive regulation of immune system process!0.0308132798303632!1997$GO:0005643!nuclear pore!0.0308132798303632!10482$GO:0050658!RNA transport!0.0308132798303632!10482$GO:0051236!establishment of RNA localization!0.0308132798303632!10482$GO:0050657!nucleic acid transport!0.0308132798303632!10482$GO:0006403!RNA localization!0.0308132798303632!10482$GO:0046930!pore complex!0.0308132798303632!10482$GO:0050776!regulation of immune response!0.0308132798303632!1997$GO:0002682!regulation of immune system process!0.0308132798303632!1997$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.0308132798303632!10482$GO:0051240!positive regulation of multicellular organismal process!0.0308132798303632!1997$GO:0044453!nuclear membrane part!0.0314082394328219!10482$GO:0001816!cytokine production!0.0314082394328219!1997$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0376154392284251!1997$GO:0031965!nuclear membrane!0.0391808275779859!10482$GO:0006913!nucleocytoplasmic transport!0.0391808275779859!10482$GO:0051169!nuclear transport!0.0391808275779859!10482$GO:0005635!nuclear envelope!0.0475384409643424!10482
|id=C686
|id=C686
}}
}}

Revision as of 17:41, 18 May 2012


Full id: C686_CD14_immature_CD19_Eosinophils_migratory_Mast_Basophils



Phase1 CAGE Peaks

Hg19::chr11:62572901..62572919,-p1@NXF1
Hg19::chr11:65153902..65153912,-p@chr11:65153902..65153912
-
Hg19::chr11:9482656..9482660,+p@chr11:9482656..9482660
+
Hg19::chr12:111020479..111020516,-p@chr12:111020479..111020516
-
Hg19::chr12:111020600..111020632,+p@chr12:111020600..111020632
+
Hg19::chr13:41635806..41635828,-p14@ELF1
Hg19::chr1:200638744..200638765,+p1@ENST00000422640
Hg19::chr1:6845035..6845053,-p1@ENST00000442889
Hg19::chr4:106394656..106394684,+p@chr4:106394656..106394684
+
Hg19::chr6:112126045..112126050,+p@chr6:112126045..112126050
+
Hg19::chr6:14117995..14118012,+p1@CD83
Hg19::chr7:151047008..151047012,-p@chr7:151047008..151047012
-


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:0016973poly(A)+ mRNA export from nucleus0.00794725374557758
GO:0050858negative regulation of antigen receptor-mediated signaling pathway0.00794725374557758
GO:0050860negative regulation of T cell receptor signaling pathway0.00794725374557758
GO:0042405nuclear inclusion body0.00794725374557758
GO:0016234inclusion body0.0105950906474368
GO:0050856regulation of T cell receptor signaling pathway0.0105950906474368
GO:0005487nucleocytoplasmic transporter activity0.0105950906474368
GO:0050854regulation of antigen receptor-mediated signaling pathway0.0132426936896461
GO:0050852T cell receptor signaling pathway0.0200070579879434
GO:0006406mRNA export from nucleus0.0211733427389052
GO:0050851antigen receptor-mediated signaling pathway0.0211733427389052
GO:0002429immune response-activating cell surface receptor signaling pathway0.0211733427389052
GO:0006405RNA export from nucleus0.0211733427389052
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0211733427389052
GO:0002757immune response-activating signal transduction0.0211733427389052
GO:0002764immune response-regulating signal transduction0.0211733427389052
GO:0003729mRNA binding0.0211733427389052
GO:0006955immune response0.0228402138005044
GO:0001817regulation of cytokine production0.0228402138005044
GO:0051168nuclear export0.0232838193519774
GO:0002376immune system process0.027740075393911
GO:0002253activation of immune response0.0308132798303632
GO:0006959humoral immune response0.0308132798303632
GO:0051028mRNA transport0.0308132798303632
GO:0050778positive regulation of immune response0.0308132798303632
GO:0002684positive regulation of immune system process0.0308132798303632
GO:0005643nuclear pore0.0308132798303632
GO:0050658RNA transport0.0308132798303632
GO:0051236establishment of RNA localization0.0308132798303632
GO:0050657nucleic acid transport0.0308132798303632
GO:0006403RNA localization0.0308132798303632
GO:0046930pore complex0.0308132798303632
GO:0050776regulation of immune response0.0308132798303632
GO:0002682regulation of immune system process0.0308132798303632
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0308132798303632
GO:0051240positive regulation of multicellular organismal process0.0308132798303632
GO:0044453nuclear membrane part0.0314082394328219
GO:0001816cytokine production0.0314082394328219
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0376154392284251
GO:0031965nuclear membrane0.0391808275779859
GO:0006913nucleocytoplasmic transport0.0391808275779859
GO:0051169nuclear transport0.0391808275779859
GO:0005635nuclear envelope0.0475384409643424



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

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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.