Personal tools

Coexpression cluster:C446: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C446_Neutrophils_Mast_Eosinophils_Whole_CD14_immature_optic |id=C446 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C446_Neutrophils_Mast_Eosinophils_Whole_CD14_immature_optic
|full_id=C446_Neutrophils_Mast_Eosinophils_Whole_CD14_immature_optic
|gostat_on_coexpression_clusters=GO:0005515!protein binding!0.0198265617681682!79890;7128;9693;55534;9586;5023;2353$GO:0006366!transcription from RNA polymerase II promoter!0.0222516553977654!55534;9586;2353$GO:0065007!biological regulation!0.0222516553977654!7128;9693;55534;9586;5023;2353$GO:0017034!Rap guanyl-nucleotide exchange factor activity!0.0222516553977654!9693$GO:0046582!Rap GTPase activator activity!0.023800322236145!9693$GO:0004931!ATP-gated cation channel activity!0.023800322236145!5023$GO:0035249!synaptic transmission, glutamatergic!0.023800322236145!5023$GO:0045893!positive regulation of transcription, DNA-dependent!0.023800322236145!55534;9586$GO:0043124!negative regulation of I-kappaB kinase/NF-kappaB cascade!0.0265035690185179!7128$GO:0007165!signal transduction!0.0265035690185179!79890;7128;9693;55534;5023$GO:0045941!positive regulation of transcription!0.0265035690185179!55534;9586$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0265035690185179!55534;9586$GO:0007154!cell communication!0.0296771541767025!79890;7128;9693;55534;5023$GO:0050794!regulation of cellular process!0.0296771541767025!7128;9693;55534;9586;2353$GO:0005096!GTPase activator activity!0.0296771541767025!79890;9693$GO:0031325!positive regulation of cellular metabolic process!0.0296771541767025!55534;9586$GO:0046983!protein dimerization activity!0.0296771541767025!9586;2353$GO:0007243!protein kinase cascade!0.0296771541767025!7128;9693$GO:0009893!positive regulation of metabolic process!0.0303613989977837!55534;9586$GO:0050789!regulation of biological process!0.0315500390975979!7128;9693;55534;9586;2353$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.0320551948780199!55534;2353$GO:0042310!vasoconstriction!0.0323260544063619!5023$GO:0044451!nucleoplasm part!0.0323557424108025!55534;2353$GO:0008047!enzyme activator activity!0.0323557424108025!79890;9693$GO:0007270!nerve-nerve synaptic transmission!0.0337717794615979!5023$GO:0005654!nucleoplasm!0.0364885636811877!55534;2353$GO:0006305!DNA alkylation!0.0364885636811877!2353$GO:0006306!DNA methylation!0.0364885636811877!2353$GO:0006304!DNA modification!0.0428701763320134!2353
|id=C446
|id=C446
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C446_Neutrophils_Mast_Eosinophils_Whole_CD14_immature_optic



Phase1 CAGE Peaks

Hg19::chr11:59521653..59521681,+p@chr11:59521653..59521681
+
Hg19::chr14:75746340..75746368,+p3@FOS
Hg19::chr14:93118094..93118129,+p8@RIN3
Hg19::chr14:93118130..93118140,+p18@RIN3
Hg19::chr16:27325997..27326036,+p@chr16:27325997..27326036
+
Hg19::chr17:3819751..3819767,-p1@P2RX1
Hg19::chr17:4802910..4802929,+p5@C17orf107
Hg19::chr1:231665876..231665886,-p@chr1:231665876..231665886
-
Hg19::chr1:231666076..231666093,+p@chr1:231666076..231666093
+
Hg19::chr20:34357224..34357250,+p@chr20:34357224..34357250
+
Hg19::chr2:208029288..208029307,+p@chr2:208029288..208029307
+
Hg19::chr2:232469321..232469404,-p@chr2:232469321..232469404
-
Hg19::chr2:43358229..43358245,-p@chr2:43358229..43358245
-
Hg19::chr2:43453036..43453081,-p@chr2:43453036..43453081
-
Hg19::chr2:43453083..43453099,-p@chr2:43453083..43453099
-
Hg19::chr4:141074616..141074637,-p7@MAML3
Hg19::chr4:160024275..160024320,+p@chr4:160024275..160024320
+
Hg19::chr4:160024323..160024354,+p@chr4:160024323..160024354
+
Hg19::chr4:160025300..160025318,+p9@RAPGEF2
Hg19::chr4:6918626..6918641,+p@chr4:6918626..6918641
+
Hg19::chr6:138188551..138188562,+p5@TNFAIP3
Hg19::chr7:28725740..28725778,+p1@CREB5


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:0005515protein binding0.0198265617681682
GO:0006366transcription from RNA polymerase II promoter0.0222516553977654
GO:0065007biological regulation0.0222516553977654
GO:0017034Rap guanyl-nucleotide exchange factor activity0.0222516553977654
GO:0046582Rap GTPase activator activity0.023800322236145
GO:0004931ATP-gated cation channel activity0.023800322236145
GO:0035249synaptic transmission, glutamatergic0.023800322236145
GO:0045893positive regulation of transcription, DNA-dependent0.023800322236145
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0265035690185179
GO:0007165signal transduction0.0265035690185179
GO:0045941positive regulation of transcription0.0265035690185179
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0265035690185179
GO:0007154cell communication0.0296771541767025
GO:0050794regulation of cellular process0.0296771541767025
GO:0005096GTPase activator activity0.0296771541767025
GO:0031325positive regulation of cellular metabolic process0.0296771541767025
GO:0046983protein dimerization activity0.0296771541767025
GO:0007243protein kinase cascade0.0296771541767025
GO:0009893positive regulation of metabolic process0.0303613989977837
GO:0050789regulation of biological process0.0315500390975979
GO:0006357regulation of transcription from RNA polymerase II promoter0.0320551948780199
GO:0042310vasoconstriction0.0323260544063619
GO:0044451nucleoplasm part0.0323557424108025
GO:0008047enzyme activator activity0.0323557424108025
GO:0007270nerve-nerve synaptic transmission0.0337717794615979
GO:0005654nucleoplasm0.0364885636811877
GO:0006305DNA alkylation0.0364885636811877
GO:0006306DNA methylation0.0364885636811877
GO:0006304DNA modification0.0428701763320134



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.