Sex Specific Gene Regulation and Expression QTLs in Mouse Macrophages from a Strain Intercross
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Mendeley | Further Information

{"title"=>"Sex Specific Gene Regulation and Expression QTLs in Mouse Macrophages from a Strain Intercross", "type"=>"journal", "authors"=>[{"first_name"=>"Jeffrey M.", "last_name"=>"Bhasin"}, {"first_name"=>"Enakshi", "last_name"=>"Chakrabarti"}, {"first_name"=>"Dao-Quan", "last_name"=>"Peng"}, {"first_name"=>"Aneesh", "last_name"=>"Kulkarni"}, {"first_name"=>"Xi", "last_name"=>"Chen"}, {"first_name"=>"Jonathan D.", "last_name"=>"Smith"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"18197246", "doi"=>"10.1371/journal.pone.0001435", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"1932-6203"}, "id"=>"d0074929-9058-317c-ac99-ad06a648918a", "abstract"=>"BACKGROUND: A powerful way to identify genes for complex traits it to combine genetic and genomic methods. Many trait quantitative trait loci (QTLs) for complex traits are sex specific, but the reason for this is not well understood.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: RNA was prepared from bone marrow derived macrophages of 93 female and 114 male F(2) mice derived from a strain intercross between apoE-deficient mice on the AKR and DBA/2 genetic backgrounds, and was subjected to transcriptome profiling using microarrays. A high density genome scan was performed using a mouse SNP chip, and expression QTLs (eQTLs) were located for expressed transcripts. Using suggestive and significant LOD score cutoffs of 3.0 and 4.3, respectively, thousands of eQTLs in the female and male cohorts were identified. At the suggestive LOD threshold the majority of the eQTLs were trans eQTLs, mapping unlinked to the position of the gene. Cis eQTLs, which mapped to the location of the gene, had much higher LOD scores than trans eQTLs, indicating their more direct effect on gene expression. The majority of cis eQTLs were common to both males and females, but only approximately 1% of the trans eQTLs were shared by both sexes. At the significant LOD threshold, the majority of eQTLs were cis eQTLs, which were mostly sex-shared, while the trans eQTLs were overwhelmingly sex-specific. Pooling the male and female data, 31% of expressed transcripts were expressed at different levels in males vs. females after correction for multiple testing.\\n\\nCONCLUSIONS/SIGNIFICANCE: These studies demonstrate a large sex effect on gene expression and trans regulation, under conditions where male and female derived cells were cultured ex vivo and thus without the influence of endogenous sex steroids. These data suggest that eQTL data from male and female mice should be analyzed separately, as many effects, such as trans regulation are sex specific.", "link"=>"http://www.mendeley.com/research/sex-specific-gene-regulation-expression-qtls-mouse-macrophages-strain-intercross", "reader_count"=>17, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Student > Doctoral Student"=>2, "Researcher"=>3, "Student > Ph. D. Student"=>6, "Other"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Student > Doctoral Student"=>2, "Researcher"=>3, "Student > Ph. D. Student"=>6, "Other"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>13, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/938688"], "description"=>"<p>Bone marrow derived macrophage eQTLs with LOD≥3.0 were mapped to partially overlapping 20 Mb bins in female (A) and male (B) F<sub>2</sub> mice. The horizontal dotted line denotes the arbitrary cutoff for eQTL hotspots. eQTLs for sex biased transcripts with LOD≥3.0 were mapped to partially overlapping 20 Mb bins in female (C) and male (D) F<sub>2</sub> mice.</p>", "links"=>[], "tags"=>["genetics and genomics/animal genetics", "genetics and genomics/complex traits", "genetics and genomics/gene expression"], "article_id"=>609129, "categories"=>["Genetics"], "users"=>["Jeffrey M. Bhasin", "Enakshi Chakrabarti", "Dao-Quan Peng", "Aneesh Kulkarni", "Xi Chen", "Jonathan D. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001435.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomic_location_of_eQTLs_/609129", "title"=>"Genomic location of eQTLs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-01-16 02:32:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/938971"], "description"=>"<p>(Only probes with average expression value greater than 150 used in correlations)</p>", "links"=>[], "tags"=>["chromosome", "hotspot", "cis", "eqtls", "308", "trans"], "article_id"=>609411, "categories"=>["Genetics"], "users"=>["Jeffrey M. Bhasin", "Enakshi Chakrabarti", "Dao-Quan Peng", "Aneesh Kulkarni", "Xi Chen", "Jonathan D. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001435.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlations_of_expression_data_for_chromosome_1_hotspot_cis_eQTLs_with_308_trans_eQTLs_in_males_/609411", "title"=>"Correlations of expression data for chromosome 1 hotspot cis eQTLs with 308 trans eQTLs in males.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-01-16 02:36:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/938797"], "description"=>"#<p>based upon a pool of transcripts using the combined male and female expression data. Values for permuted data are mean+S.D. for 5 separate gender permutations.</p>", "links"=>[], "tags"=>["trans", "mice"], "article_id"=>609245, "categories"=>["Genetics"], "users"=>["Jeffrey M. Bhasin", "Enakshi Chakrabarti", "Dao-Quan Peng", "Aneesh Kulkarni", "Xi Chen", "Jonathan D. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001435.t005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cis_and_Trans_eQTLs_LOD_4_3_in_male_and_female_mice_with_and_without_5_gender_permutations_/609245", "title"=>"Cis and Trans eQTLs≥LOD 4.3 in male and female mice with and without 5 gender permutations<sup>#</sup>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-01-16 02:34:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/938933"], "description"=>"<p>Correlations of expression data for chromosome 16 hotspot cis eQTLs with 379 trans eQTLs in males.</p>", "links"=>[], "tags"=>["chromosome", "16", "hotspot", "cis", "eqtls", "379", "trans"], "article_id"=>609372, "categories"=>["Genetics"], "users"=>["Jeffrey M. Bhasin", "Enakshi Chakrabarti", "Dao-Quan Peng", "Aneesh Kulkarni", "Xi Chen", "Jonathan D. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001435.t003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlations_of_expression_data_for_chromosome_16_hotspot_cis_eQTLs_with_379_trans_eQTLs_in_males_/609372", "title"=>"Correlations of expression data for chromosome 16 hotspot cis eQTLs with 379 trans eQTLs in males.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-01-16 02:36:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/938891"], "description"=>"<p>eQTL summary in female and male F<sub>2</sub> mice</p>", "links"=>[], "tags"=>["genetics and genomics/animal genetics", "genetics and genomics/complex traits", "genetics and genomics/gene expression"], "article_id"=>609337, "categories"=>["Genetics"], "users"=>["Jeffrey M. Bhasin", "Enakshi Chakrabarti", "Dao-Quan Peng", "Aneesh Kulkarni", "Xi Chen", "Jonathan D. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001435.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_eQTL_summary_in_female_and_male_F_2_mice_/609337", "title"=>"eQTL summary in female and male F<sub>2</sub> mice", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-01-16 02:35:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/938832"], "description"=>"<p>eQTLs shared by male and female F<sub>2</sub> mice.</p>", "links"=>[], "tags"=>["genetics and genomics/animal genetics", "genetics and genomics/complex traits", "genetics and genomics/gene expression"], "article_id"=>609271, "categories"=>["Genetics"], "users"=>["Jeffrey M. Bhasin", "Enakshi Chakrabarti", "Dao-Quan Peng", "Aneesh Kulkarni", "Xi Chen", "Jonathan D. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001435.t004", "stats"=>{"downloads"=>4, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_eQTLs_shared_by_male_and_female_F_2_mice_/609271", "title"=>"eQTLs shared by male and female F<sub>2</sub> mice.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-01-16 02:34:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/938861"], "description"=>"<p>Number and fold-effects of transcripts with sex biased expression with p<2.27×10<sup>−6</sup>.</p>", "links"=>[], "tags"=>["fold-effects", "transcripts", "biased"], "article_id"=>609304, "categories"=>["Genetics"], "users"=>["Jeffrey M. Bhasin", "Enakshi Chakrabarti", "Dao-Quan Peng", "Aneesh Kulkarni", "Xi Chen", "Jonathan D. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001435.t006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_and_fold_effects_of_transcripts_with_sex_biased_expression_with_p_8722_6_/609304", "title"=>"Number and fold-effects of transcripts with sex biased expression with p<2.27×10<sup>−6</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-01-16 02:35:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/462697", "https://ndownloader.figshare.com/files/462733", "https://ndownloader.figshare.com/files/462756", "https://ndownloader.figshare.com/files/462775", "https://ndownloader.figshare.com/files/462796", "https://ndownloader.figshare.com/files/462812", "https://ndownloader.figshare.com/files/462830", "https://ndownloader.figshare.com/files/462850", "https://ndownloader.figshare.com/files/462867", "https://ndownloader.figshare.com/files/462887"], "description"=>"<div><h3>Background</h3><p>A powerful way to identify genes for complex traits it to combine genetic and genomic methods. Many trait quantitative trait loci (QTLs) for complex traits are sex specific, but the reason for this is not well understood.</p><h3>Methodology/Principal Findings</h3><p>RNA was prepared from bone marrow derived macrophages of 93 female and 114 male F<sub>2</sub> mice derived from a strain intercross between apoE-deficient mice on the AKR and DBA/2 genetic backgrounds, and was subjected to transcriptome profiling using microarrays. A high density genome scan was performed using a mouse SNP chip, and expression QTLs (eQTLs) were located for expressed transcripts. Using suggestive and significant LOD score cutoffs of 3.0 and 4.3, respectively, thousands of eQTLs in the female and male cohorts were identified. At the suggestive LOD threshold the majority of the eQTLs were trans eQTLs, mapping unlinked to the position of the gene. Cis eQTLs, which mapped to the location of the gene, had much higher LOD scores than trans eQTLs, indicating their more direct effect on gene expression. The majority of cis eQTLs were common to both males and females, but only ∼1% of the trans eQTLs were shared by both sexes. At the significant LOD threshold, the majority of eQTLs were cis eQTLs, which were mostly sex-shared, while the trans eQTLs were overwhelmingly sex-specific. Pooling the male and female data, 31% of expressed transcripts were expressed at different levels in males vs. females after correction for multiple testing.</p><h3>Conclusions/Significance</h3><p>These studies demonstrate a large sex effect on gene expression and trans regulation, under conditions where male and female derived cells were cultured ex vivo and thus without the influence of endogenous sex steroids. These data suggest that eQTL data from male and female mice should be analyzed separately, as many effects, such as trans regulation are sex specific.</p></div>", "links"=>[], "tags"=>["qtls", "macrophages", "intercross"], "article_id"=>151205, "categories"=>["Genetics"], "users"=>["Jeffrey M. Bhasin", "Enakshi Chakrabarti", "Dao-Quan Peng", "Aneesh Kulkarni", "Xi Chen", "Jonathan D. Smith"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0001435.s001", "https://dx.doi.org/10.1371/journal.pone.0001435.s002", "https://dx.doi.org/10.1371/journal.pone.0001435.s003", "https://dx.doi.org/10.1371/journal.pone.0001435.s004", "https://dx.doi.org/10.1371/journal.pone.0001435.s005", "https://dx.doi.org/10.1371/journal.pone.0001435.s006", "https://dx.doi.org/10.1371/journal.pone.0001435.s007", "https://dx.doi.org/10.1371/journal.pone.0001435.s008", "https://dx.doi.org/10.1371/journal.pone.0001435.s009", "https://dx.doi.org/10.1371/journal.pone.0001435.s010"], "stats"=>{"downloads"=>18, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Sex_Specific_Gene_Regulation_and_Expression_QTLs_in_Mouse_Macrophages_from_a_Strain_Intercross/151205", "title"=>"Sex Specific Gene Regulation and Expression QTLs in Mouse Macrophages from a Strain Intercross", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-01-16 00:20:05"}

PMC Usage Stats | Further Information

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Relative Metric

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