Personal tools

Coexpression cluster:C306: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C306_CD4_CD8_Neutrophils_Natural_CD19_CD14_Peripheral |id=C306 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C306_CD4_CD8_Neutrophils_Natural_CD19_CD14_Peripheral
|full_id=C306_CD4_CD8_Neutrophils_Natural_CD19_CD14_Peripheral
|gostat_on_coexpression_clusters=GO:0043489!RNA stabilization!0.00193016097290205!26986$GO:0048255!mRNA stabilization!0.00193016097290205!26986$GO:0008494!translation activator activity!0.00193016097290205!26986$GO:0008143!poly(A) binding!0.00193016097290205!26986$GO:0043487!regulation of RNA stability!0.00193016097290205!26986$GO:0043488!regulation of mRNA stability!0.00193016097290205!26986$GO:0006378!mRNA polyadenylation!0.00193016097290205!26986$GO:0043631!RNA polyadenylation!0.00233525648573335!26986$GO:0031124!mRNA 3'-end processing!0.00233525648573335!26986$GO:0031123!RNA 3'-end processing!0.00250206052042859!26986$GO:0051252!regulation of RNA metabolic process!0.00250206052042859!26986$GO:0003727!single-stranded RNA binding!0.00250206052042859!26986$GO:0003729!mRNA binding!0.00392631035513409!26986$GO:0005681!spliceosome!0.0149051319574103!26986$GO:0008135!translation factor activity, nucleic acid binding!0.0201165665842458!26986$GO:0008380!RNA splicing!0.0211111356411162!26986$GO:0006397!mRNA processing!0.0241080890144825!26986$GO:0016071!mRNA metabolic process!0.0285234899328859!26986$GO:0006396!RNA processing!0.0414815296807897!26986
|id=C306
|id=C306
}}
}}

Revision as of 17:38, 18 May 2012


Full id: C306_CD4_CD8_Neutrophils_Natural_CD19_CD14_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:112662692..112662695,+p@chr10:112662692..112662695
+
Hg19::chr10:120969026..120969030,+p@chr10:120969026..120969030
+
Hg19::chr10:70101463..70101469,+p14@HNRNPH3
Hg19::chr11:64540106..64540118,-p@chr11:64540106..64540118
-
Hg19::chr11:66412411..66412415,+p@chr11:66412411..66412415
+
Hg19::chr12:496389..496393,-p@chr12:496389..496393
-
Hg19::chr12:92506284..92506289,-p@chr12:92506284..92506289
-
Hg19::chr12:92517978..92517981,-p@chr12:92517978..92517981
-
Hg19::chr12:92521923..92521946,-p@chr12:92521923..92521946
-
Hg19::chr12:92525764..92525779,-p@chr12:92525764..92525779
-
Hg19::chr12:92529815..92529831,-p@chr12:92529815..92529831
-
Hg19::chr16:2805857..2805868,+p3@AB384460
Hg19::chr16:31196235..31196241,+p@chr16:31196235..31196241
+
Hg19::chr17:38720548..38720562,-p@chr17:38720548..38720562
-
Hg19::chr17:8397217..8397222,+p@chr17:8397217..8397222
+
Hg19::chr18:2734660..2734665,+p@chr18:2734660..2734665
+
Hg19::chr18:9218683..9218688,+p@chr18:9218683..9218688
+
Hg19::chr1:14076901..14076905,+p@chr1:14076901..14076905
+
Hg19::chr1:14084295..14084298,+p@chr1:14084295..14084298
+
Hg19::chr1:171519143..171519147,+p@chr1:171519143..171519147
+
Hg19::chr20:34304613..34304617,-p@chr20:34304613..34304617
-
Hg19::chr20:42837055..42837068,-p@chr20:42837055..42837068
-
Hg19::chr21:34931287..34931294,+p@chr21:34931287..34931294
+
Hg19::chr2:238604341..238604365,+p@chr2:238604341..238604365
+
Hg19::chr2:30378335..30378347,+p@chr2:30378335..30378347
+
Hg19::chr2:47171535..47171539,+p@chr2:47171535..47171539
+
Hg19::chr2:96959867..96959871,-p@chr2:96959867..96959871
-
Hg19::chr3:119181738..119181740,-p@chr3:119181738..119181740
-
Hg19::chr3:150332211..150332217,+p@chr3:150332211..150332217
+
Hg19::chr3:156869602..156869621,-p@chr3:156869602..156869621
-
Hg19::chr3:9932605..9932620,-p@chr3:9932605..9932620
-
Hg19::chr4:103713093..103713096,-p@chr4:103713093..103713096
-
Hg19::chr5:130638530..130638534,+p@chr5:130638530..130638534
+
Hg19::chr5:32592687..32592708,+p@chr5:32592687..32592708
+
Hg19::chr6:139489578..139489582,+p@chr6:139489578..139489582
+
Hg19::chr7:26234405..26234412,-p@chr7:26234405..26234412
-
Hg19::chr8:101725008..101725030,-p16@PABPC1
Hg19::chr8:101728081..101728097,-p22@PABPC1
Hg19::chr8:101959111..101959114,-p@chr8:101959111..101959114
-


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:0043489RNA stabilization0.00193016097290205
GO:0048255mRNA stabilization0.00193016097290205
GO:0008494translation activator activity0.00193016097290205
GO:0008143poly(A) binding0.00193016097290205
GO:0043487regulation of RNA stability0.00193016097290205
GO:0043488regulation of mRNA stability0.00193016097290205
GO:0006378mRNA polyadenylation0.00193016097290205
GO:0043631RNA polyadenylation0.00233525648573335
GO:0031124mRNA 3'-end processing0.00233525648573335
GO:0031123RNA 3'-end processing0.00250206052042859
GO:0051252regulation of RNA metabolic process0.00250206052042859
GO:0003727single-stranded RNA binding0.00250206052042859
GO:0003729mRNA binding0.00392631035513409
GO:0005681spliceosome0.0149051319574103
GO:0008135translation factor activity, nucleic acid binding0.0201165665842458
GO:0008380RNA splicing0.0211111356411162
GO:0006397mRNA processing0.0241080890144825
GO:0016071mRNA metabolic process0.0285234899328859
GO:0006396RNA processing0.0414815296807897



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C306&oldid=1702935"