Cis and Trans Effects of Human Genomic Variants on Gene Expression
Publication Date
July 10, 2014
Journal
PLOS Genetics
Authors
Julien Bryois, Alfonso Buil, David M. Evans, John P. Kemp, et al
Volume
10
Issue
7
Pages
e1004461
DOI
http://doi.org/10.1371/journal.pgen.1004461
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1004461
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25010687
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091791
Europe PMC
http://europepmc.org/abstract/MED/25010687
Web of Science
000339902600019
Scopus
84905484562
Mendeley
http://www.mendeley.com/research/cis-trans-effects-human-genomic-variants-gene-expression
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Mendeley | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1588105"], "description"=>"<p>(A) Histogram of the proportion of probes (π1) affected in trans by each cis-eQTL that could be detected with a very large sample size. The cis-eQTLs of several genes is highlighted in black. (B) Histogram of the number of genes significantly affected in trans by cis-eQTLs (5% FDR) detected with 869 individuals.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Gene regulatory networks", "genetics", "genomics", "Functional genomics", "gene expression", "Human genetics"], "article_id"=>1099753, "categories"=>["Biological Sciences"], "users"=>["Julien Bryois", "Alfonso Buil", "David M. Evans", "John P. Kemp", "Stephen B. Montgomery", "Donald F. Conrad", "Karen M. Ho", "Susan Ring", "Matthew Hurles", "Panos Deloukas", "George Davey Smith", "Emmanouil T. Dermitzakis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004461.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trans_effects_of_cis_eQTLs_/1099753", "title"=>"Trans-effects of cis-eQTLs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-10 03:24:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/1588095"], "description"=>"<p>(A) Histogram of heritability explained by the best cis-eQTL and (B) all independent cis-eQTLs for genes with more than one cis-eQTL. (C) Heritability explained by independent cis-eQTLs compared to the heritability explained by their best cis-eQTL for genes with more than one cis-eQTL. (D) Heritability of genes with one cis-eQTL (red) and more than one cis-eQTL (black) compared to heritabilty explained by all available eQTLs.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Gene regulatory networks", "genetics", "genomics", "Functional genomics", "gene expression", "Human genetics", "trans", "genomic", "variants"], "article_id"=>1099751, "categories"=>["Biological Sciences"], "users"=>["Julien Bryois", "Alfonso Buil", "David M. Evans", "John P. Kemp", "Stephen B. Montgomery", "Donald F. Conrad", "Karen M. Ho", "Susan Ring", "Matthew Hurles", "Panos Deloukas", "George Davey Smith", "Emmanouil T. Dermitzakis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004461.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cis_and_Trans_Effects_of_Human_Genomic_Variants_on_Gene_Expression_Figure_1_/1099751", "title"=>"Cis and Trans Effects of Human Genomic Variants on Gene Expression - Figure 1", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-10 03:24:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/1588104"], "description"=>"<p>Error bars represent the 5% and 95% confidence interval and lines show the best polynomial fit of the data.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Gene regulatory networks", "genetics", "genomics", "Functional genomics", "gene expression", "Human genetics", "sharing", "cis-eqtls", "alspac", "lcls", "muther", "cohort", "adipose", "tissues"], "article_id"=>1099752, "categories"=>["Biological Sciences"], "users"=>["Julien Bryois", "Alfonso Buil", "David M. Evans", "John P. Kemp", "Stephen B. Montgomery", "Donald F. Conrad", "Karen M. Ho", "Susan Ring", "Matthew Hurles", "Panos Deloukas", "George Davey Smith", "Emmanouil T. Dermitzakis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004461.g002", "stats"=>{"downloads"=>3, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tissue_sharing_960_1_of_cis_eQTLs_between_ALSPAC_LCLs_and_cis_eQTLs_detected_by_the_MUTHER_cohort_in_LCLs_black_skin_red_and_adipose_tissues_green_tissues_in_function_of_the_ALSPAC_sample_size_/1099752", "title"=>"Tissue sharing (π1) of cis-eQTLs between ALSPAC LCLs and cis-eQTLs detected by the MUTHER cohort in LCLs (black), skin (red) and adipose tissues (green) tissues in function of the ALSPAC sample size.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-10 03:24:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/1588110", "https://ndownloader.figshare.com/files/1588111", "https://ndownloader.figshare.com/files/1588112", "https://ndownloader.figshare.com/files/1588113", "https://ndownloader.figshare.com/files/1588114", "https://ndownloader.figshare.com/files/1588115", "https://ndownloader.figshare.com/files/1588116", "https://ndownloader.figshare.com/files/1588117", "https://ndownloader.figshare.com/files/1588118", "https://ndownloader.figshare.com/files/1588119", "https://ndownloader.figshare.com/files/1588120", "https://ndownloader.figshare.com/files/1588121", "https://ndownloader.figshare.com/files/1588122", "https://ndownloader.figshare.com/files/1588123", "https://ndownloader.figshare.com/files/1588124", "https://ndownloader.figshare.com/files/1588125"], "description"=>"<div><p>Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation. In order to detect genetic variations affecting gene expression, we performed association analysis of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with gene expression measured in 869 lymphoblastoid cell lines of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort in cis and in trans. We discovered that 3,534 genes (false discovery rate (FDR) = 5%) are affected by an expression quantitative trait locus (eQTL) in cis and 48 genes are affected in trans. We observed that CNVs are more likely to be eQTLs than SNPs. In addition, we found that variants associated to complex traits and diseases are enriched for trans-eQTLs and that trans-eQTLs are enriched for cis-eQTLs. As a variant affecting both a gene in cis and in trans suggests that the cis gene is functionally linked to the trans gene expression, we looked specifically for trans effects of cis-eQTLs. We discovered that 26 cis-eQTLs are associated to 92 genes in trans with the cis-eQTLs of the transcriptions factors BATF3 and HMX2 affecting the most genes. We then explored if the variation of the level of expression of the cis genes were causally affecting the level of expression of the trans genes and discovered several causal relationships between variation in the level of expression of the cis gene and variation of the level of expression of the trans gene. This analysis shows that a large sample size allows the discovery of secondary effects of human variations on gene expression that can be used to construct short directed gene regulatory networks.</p></div>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Gene regulatory networks", "genetics", "genomics", "Functional genomics", "gene expression", "Human genetics", "trans", "genomic", "variants"], "article_id"=>1099758, "categories"=>["Biological Sciences"], "users"=>["Julien Bryois", "Alfonso Buil", "David M. Evans", "John P. Kemp", "Stephen B. Montgomery", "Donald F. Conrad", "Karen M. Ho", "Susan Ring", "Matthew Hurles", "Panos Deloukas", "George Davey Smith", "Emmanouil T. Dermitzakis"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004461.s001", "https://dx.doi.org/10.1371/journal.pgen.1004461.s002", "https://dx.doi.org/10.1371/journal.pgen.1004461.s003", "https://dx.doi.org/10.1371/journal.pgen.1004461.s004", "https://dx.doi.org/10.1371/journal.pgen.1004461.s005", "https://dx.doi.org/10.1371/journal.pgen.1004461.s006", "https://dx.doi.org/10.1371/journal.pgen.1004461.s007", "https://dx.doi.org/10.1371/journal.pgen.1004461.s008", "https://dx.doi.org/10.1371/journal.pgen.1004461.s009", "https://dx.doi.org/10.1371/journal.pgen.1004461.s010", "https://dx.doi.org/10.1371/journal.pgen.1004461.s011", "https://dx.doi.org/10.1371/journal.pgen.1004461.s012", "https://dx.doi.org/10.1371/journal.pgen.1004461.s013", "https://dx.doi.org/10.1371/journal.pgen.1004461.s014", "https://dx.doi.org/10.1371/journal.pgen.1004461.s015", "https://dx.doi.org/10.1371/journal.pgen.1004461.s016"], "stats"=>{"downloads"=>59, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cis_and_Trans_Effects_of_Human_Genomic_Variants_on_Gene_Expression_/1099758", "title"=>"Cis and Trans Effects of Human Genomic Variants on Gene Expression", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-07-10 03:24:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/1588107"], "description"=>"<p>Causal directed relationships between variation in level of expression of the cis gene and variation in the level of expression of the trans gene.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Gene regulatory networks", "genetics", "genomics", "Functional genomics", "gene expression", "Human genetics", "directed", "relationships", "cis", "trans"], "article_id"=>1099755, "categories"=>["Biological Sciences"], "users"=>["Julien Bryois", "Alfonso Buil", "David M. Evans", "John P. Kemp", "Stephen B. Montgomery", "Donald F. Conrad", "Karen M. Ho", "Susan Ring", "Matthew Hurles", "Panos Deloukas", "George Davey Smith", "Emmanouil T. Dermitzakis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004461.t002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Causal_directed_relationships_between_variation_in_level_of_expression_of_the_cis_gene_and_variation_in_the_level_of_expression_of_the_trans_gene_/1099755", "title"=>"Causal directed relationships between variation in level of expression of the cis gene and variation in the level of expression of the trans gene.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-10 03:24:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/1588106"], "description"=>"<p>Top 15 trans-eQTLs (5% FDR).</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Gene regulatory networks", "genetics", "genomics", "Functional genomics", "gene expression", "Human genetics", "15", "trans-eqtls"], "article_id"=>1099754, "categories"=>["Biological Sciences"], "users"=>["Julien Bryois", "Alfonso Buil", "David M. Evans", "John P. Kemp", "Stephen B. Montgomery", "Donald F. Conrad", "Karen M. Ho", "Susan Ring", "Matthew Hurles", "Panos Deloukas", "George Davey Smith", "Emmanouil T. Dermitzakis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004461.t001", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_15_trans_eQTLs_5_FDR_/1099754", "title"=>"Top 15 trans-eQTLs (5% FDR).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-10 03:24:24"}

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Relative Metric

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