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Coexpression cluster:C1765: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0048010!vascular endothelial growth factor receptor signaling pathway!0.0435920646625478!2324$GO:0030165!PDZ domain binding!0.0435920646625478!83878$GO:0005021!vascular endothelial growth factor receptor activity!0.0435920646625478!2324$GO:0006471!protein amino acid ADP-ribosylation!0.0435920646625478!9630$GO:0005834!heterotrimeric G-protein complex!0.0496118168482225!9630
|gostat_on_coexpression_clusters=GO:0048010!vascular endothelial growth factor receptor signaling pathway!0.0435920646625478!2324$GO:0030165!PDZ domain binding!0.0435920646625478!83878$GO:0005021!vascular endothelial growth factor receptor activity!0.0435920646625478!2324$GO:0006471!protein amino acid ADP-ribosylation!0.0435920646625478!9630$GO:0005834!heterotrimeric G-protein complex!0.0496118168482225!9630
|id=C1765
|id=C1765
|ontology_enrichment_celltype=CL:0000115!5.27e-17!35;CL:0002139!1.34e-16!24;CL:0002078!1.52e-14!44;CL:0000071!5.13e-12!18;CL:0002546!5.13e-12!18;CL:0000213!3.64e-10!57;CL:0000215!3.64e-10!57
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.17e-42!115;UBERON:0004111!1.73e-16!241;UBERON:0000025!6.58e-15!194;UBERON:0001049!7.82e-15!57;UBERON:0005068!7.82e-15!57;UBERON:0006241!7.82e-15!57;UBERON:0007135!7.82e-15!57;UBERON:0000477!1.05e-13!286;UBERON:0001017!2.15e-13!82;UBERON:0003080!6.70e-13!42;UBERON:0005743!1.38e-12!86;UBERON:0002346!1.46e-12!90;UBERON:0002780!2.67e-12!41;UBERON:0001890!2.67e-12!41;UBERON:0006240!2.67e-12!41;UBERON:0001986!5.13e-12!18;UBERON:0004638!5.13e-12!18;UBERON:0004852!5.13e-12!18;UBERON:0000955!5.71e-12!69;UBERON:0006238!5.71e-12!69;UBERON:0002616!6.05e-12!59;UBERON:0003075!1.30e-11!86;UBERON:0007284!1.30e-11!86;UBERON:0000073!7.27e-11!94;UBERON:0001016!7.27e-11!94;UBERON:0002020!1.75e-10!34;UBERON:0003528!1.75e-10!34;UBERON:0001893!1.88e-10!34;UBERON:0002791!3.75e-10!33;UBERON:0001869!9.85e-10!32;UBERON:0000487!2.86e-09!22;UBERON:0002619!2.88e-09!22;UBERON:0006914!3.24e-09!25;UBERON:0000119!9.94e-09!312;UBERON:0000483!2.00e-08!309;UBERON:0001950!2.03e-08!20;UBERON:0000956!9.28e-08!25;UBERON:0000203!9.28e-08!25;UBERON:0003056!1.55e-07!61
}}
}}

Revision as of 14:15, 21 May 2012


Full id: C1765_Renal_Hepatic_Endothelial_placenta_Lymphatic_breast_lung



Phase1 CAGE Peaks

Hg19::chr16:67224002..67224047,-p1@EXOC3L1
Hg19::chr19:17375527..17375538,-p2@USHBP1
Hg19::chr5:180076580..180076605,-p1@FLT4
Hg19::chr5:180076613..180076634,-p2@FLT4
Hg19::chr9:80263579..80263618,-p2@GNA14


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:0048010vascular endothelial growth factor receptor signaling pathway0.0435920646625478
GO:0030165PDZ domain binding0.0435920646625478
GO:0005021vascular endothelial growth factor receptor activity0.0435920646625478
GO:0006471protein amino acid ADP-ribosylation0.0435920646625478
GO:0005834heterotrimeric G-protein complex0.0496118168482225



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 organism1.17e-42115
anatomical conduit1.73e-16241
tube6.58e-15194
neural tube7.82e-1557
neural rod7.82e-1557
future spinal cord7.82e-1557
neural keel7.82e-1557
anatomical cluster1.05e-13286
central nervous system2.15e-1382
anterior neural tube6.70e-1342
neurectoderm1.46e-1290
regional part of forebrain2.67e-1241
forebrain2.67e-1241
future forebrain2.67e-1241
endothelium5.13e-1218
blood vessel endothelium5.13e-1218
cardiovascular system endothelium5.13e-1218
brain5.71e-1269
future brain5.71e-1269
regional part of brain6.05e-1259
neural plate1.30e-1186
presumptive neural plate1.30e-1186
regional part of nervous system7.27e-1194
nervous system7.27e-1194
gray matter1.75e-1034
brain grey matter1.75e-1034
telencephalon1.88e-1034
regional part of telencephalon3.75e-1033
cerebral hemisphere9.85e-1032
simple squamous epithelium2.86e-0922
regional part of cerebral cortex2.88e-0922
squamous epithelium3.24e-0925
cell layer9.94e-09312
epithelium2.00e-08309
neocortex2.03e-0820
cerebral cortex9.28e-0825
pallium9.28e-0825
pre-chordal neural plate1.55e-0761


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.