Dissection of a QTL Hotspot on Mouse Distal Chromosome 1 that Modulates Neurobehavioral Phenotypes and Gene Expression
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{"title"=>"Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression", "type"=>"journal", "authors"=>[{"first_name"=>"Khyobeni", "last_name"=>"Mozhui", "scopus_author_id"=>"15728161800"}, {"first_name"=>"Daniel C.", "last_name"=>"Ciobanu", "scopus_author_id"=>"6701742715"}, {"first_name"=>"Thomas", "last_name"=>"Schikorski", "scopus_author_id"=>"6603462123"}, {"first_name"=>"Xusheng", "last_name"=>"Wang", "scopus_author_id"=>"55736881700"}, {"first_name"=>"Lu", "last_name"=>"Lu", "scopus_author_id"=>"56457005100"}, {"first_name"=>"Robert W.", "last_name"=>"Williams", "scopus_author_id"=>"55674268100"}], "year"=>2008, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-57149090077", "pmid"=>"19008955", "sgr"=>"57149090077", "doi"=>"10.1371/journal.pgen.1000260", "isbn"=>"1553-7404 (Electronic)\\n1553-7390 (Linking)", "issn"=>"15537390", "pui"=>"352773681"}, "id"=>"ddc2b0a9-ad0d-3a4c-a6b6-123bfc065a97", "abstract"=>"A remarkably diverse set of traits maps to a region on mouse distal chromosome 1 (Chr 1) that corresponds to human Chr 1q21-q23. This region is highly enriched in quantitative trait loci (QTLs) that control neural and behavioral phenotypes, including motor behavior, escape latency, emotionality, seizure susceptibility (Szs1), and responses to ethanol, caffeine, pentobarbital, and haloperidol. This region also controls the expression of a remarkably large number of genes, including genes that are associated with some of the classical traits that map to distal Chr 1 (e.g., seizure susceptibility). Here, we ask whether this QTL-rich region on Chr 1 (Qrr1) consists of a single master locus or a mixture of linked, but functionally unrelated, QTLs. To answer this question and to evaluate candidate genes, we generated and analyzed several gene expression, haplotype, and sequence datasets. We exploited six complementary mouse crosses, and combed through 18 expression datasets to determine class membership of genes modulated by Qrr1. Qrr1 can be broadly divided into a proximal part (Qrr1p) and a distal part (Qrr1d), each associated with the expression of distinct subsets of genes. Qrr1d controls RNA metabolism and protein synthesis, including the expression of approximately 20 aminoacyl-tRNA synthetases. Qrr1d contains a tRNA cluster, and this is a functionally pertinent candidate for the tRNA synthetases. Rgs7 and Fmn2 are other strong candidates in Qrr1d. FMN2 protein has pronounced expression in neurons, including in the dendrites, and deletion of Fmn2 had a strong effect on the expression of few genes modulated by Qrr1d. Our analysis revealed a highly complex gene expression regulatory interval in Qrr1, composed of multiple loci modulating the expression of functionally cognate sets of genes.", "link"=>"http://www.mendeley.com/research/dissection-qtl-hotspot-mouse-distal-chromosome-1-modulates-neurobehavioral-phenotypes-gene-expressio", "reader_count"=>44, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>7, "Librarian"=>1, "Researcher"=>14, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>3, "Student > Master"=>2, "Student > Bachelor"=>3, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>7, "Librarian"=>1, "Researcher"=>14, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>3, "Student > Master"=>2, "Student > Bachelor"=>3, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>27, "Medicine and Dentistry"=>4, "Neuroscience"=>2, "Psychology"=>3, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Neuroscience"=>{"Neuroscience"=>2}, "Psychology"=>{"Psychology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Egypt"=>1, "Brazil"=>1, "Malaysia"=>1, "Slovenia"=>1, "France"=>1, "Australia"=>1, "India"=>1}, "group_count"=>2}

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  • {"files"=>["https://ndownloader.figshare.com/files/452961", "https://ndownloader.figshare.com/files/453360", "https://ndownloader.figshare.com/files/453414", "https://ndownloader.figshare.com/files/453430", "https://ndownloader.figshare.com/files/453449", "https://ndownloader.figshare.com/files/453462"], "description"=>"<div><p>A remarkably diverse set of traits maps to a region on mouse distal chromosome 1 (Chr 1) that corresponds to human Chr 1q21–q23. This region is highly enriched in quantitative trait loci (QTLs) that control neural and behavioral phenotypes, including motor behavior, escape latency, emotionality, seizure susceptibility (<em>Szs1</em>), and responses to ethanol, caffeine, pentobarbital, and haloperidol. This region also controls the expression of a remarkably large number of genes, including genes that are associated with some of the classical traits that map to distal Chr 1 (e.g., seizure susceptibility). Here, we ask whether this QTL-rich region on Chr 1 (<em>Qrr1</em>) consists of a single master locus or a mixture of linked, but functionally unrelated, QTLs. To answer this question and to evaluate candidate genes, we generated and analyzed several gene expression, haplotype, and sequence datasets. We exploited six complementary mouse crosses, and combed through 18 expression datasets to determine class membership of genes modulated by <em>Qrr1</em>. <em>Qrr1</em> can be broadly divided into a proximal part (<em>Qrr1p</em>) and a distal part (<em>Qrr1d</em>), each associated with the expression of distinct subsets of genes. <em>Qrr1d</em> controls RNA metabolism and protein synthesis, including the expression of ∼20 aminoacyl-tRNA synthetases. <em>Qrr1d</em> contains a tRNA cluster, and this is a functionally pertinent candidate for the tRNA synthetases. <em>Rgs7</em> and <em>Fmn2</em> are other strong candidates in <em>Qrr1d</em>. FMN2 protein has pronounced expression in neurons, including in the dendrites, and deletion of <em>Fmn2</em> had a strong effect on the expression of few genes modulated by <em>Qrr1d</em>. Our analysis revealed a highly complex gene expression regulatory interval in <em>Qrr1</em>, composed of multiple loci modulating the expression of functionally cognate sets of genes.</p></div>", "links"=>[], "tags"=>["dissection", "qtl", "hotspot", "distal", "chromosome", "modulates", "neurobehavioral", "phenotypes"], "article_id"=>149235, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.s001", "https://dx.doi.org/10.1371/journal.pgen.1000260.s002", "https://dx.doi.org/10.1371/journal.pgen.1000260.s003", "https://dx.doi.org/10.1371/journal.pgen.1000260.s004", "https://dx.doi.org/10.1371/journal.pgen.1000260.s005", "https://dx.doi.org/10.1371/journal.pgen.1000260.s006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Dissection_of_a_QTL_Hotspot_on_Mouse_Distal_Chromosome_1_that_Modulates_Neurobehavioral_Phenotypes_and_Gene_Expression/149235", "title"=>"Dissection of a QTL Hotspot on Mouse Distal Chromosome 1 that Modulates Neurobehavioral Phenotypes and Gene Expression", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-11-14 02:33:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/915573"], "description"=>"<p>The charts illustrate the total number of <i>trans</i>-QTLs (LOD≥4) in <i>Qrr1</i> (shaded) and in other regions of the genome (non-shaded) in three datasets—BXD cerebellum, BXD hippocampus, and B6C3H F2 brain. The smaller charts represent the <i>trans</i>-QTLs in BXD hippocampus that are also detected in BXD cerebellum, and B6C3HF2 brain datasets. Out of the 101 <i>trans</i>-QTLs common to both BXD hippocampus and cerebellum, 64 are in <i>Qrr1</i> and the remaining 37 are located in other regions of the genome. The BXD hippocampus and B6C3HF2 brain datasets have 54 common <i>trans</i>-QTLs, and almost all (52 out of 54) are in <i>Qrr1</i>.</p>", "links"=>[], "tags"=>["replicable", "trans-qtls"], "article_id"=>586023, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Highly_replicable_trans_QTLs_in_Qrr1_/586023", "title"=>"Highly replicable trans-QTLs in <i>Qrr1</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-14 01:40:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/915692"], "description"=>"<p>BXD8, BXD29, BXD62, BXD64, BXD68, and BXD84 have recombinations in <i>Qrr1</i>. <i>B</i> haplotype is assigned blue (−), <i>D</i> haplotype is assigned pink (+), and recombination regions are shown in grey. The <i>Qrr1</i> interval (in Mb scale) is shown above and approximate positions of recombination are highlighted (red). The recombinant strains collectively divide <i>Qrr1</i> into six segments (labeled 1–6), and provide six sets of informative markers. Markers are shown below and approximate positions of candidate genes (yellow bars) and tRNA clusters (orange triangles) are indicated.</p>", "links"=>[], "tags"=>["maps", "recombinant", "bxd"], "article_id"=>586144, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_maps_of_Qrr1_recombinant_BXD_strains_/586144", "title"=>"Haplotype maps of <i>Qrr1</i> recombinant BXD strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-14 01:42:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/915773"], "description"=>"<p>Mapping precision was empirically determined by measuring the distance between a <i>cis</i>-QTL peak and location of parent gene. <i>Cis</i>-QTLs in BXD Hippocampus Consortium, UMUTAffy Hippocampus, and Hamilton Eye datasets were used for this purpose. Mean gene-to-QTL peak distance (y-axis) was plotted as a function of LOD score (LOD score range on x-axis). Number of probe sets in each LOD range is shown. Mapping precision increases with increase in LOD score. The mean offset for <i>cis</i>-QTLs with LOD scores 3–4 (genome-wide adjusted p-value of 0.1–0.01) is 900 kb, and the offset decreases to 650 kb at 4–5 LOD scores (p-value of 0.01–0.001). <i>Cis</i>-QTLs with LOD scores greater than 11 (p-value<10<sup>−6</sup>) have mean offset of only 450 kb.</p>", "links"=>[], "tags"=>["precision"], "article_id"=>586231, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_QTL_mapping_precision_in_Qrr1_/586231", "title"=>"QTL mapping precision in <i>Qrr1</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-14 01:43:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/915882"], "description"=>"<p>Expression of <i>Atp5j2</i>, <i>Cplx2</i>, and <i>Nars</i> are modulated by <i>trans</i>-QTLs in <i>Qrr1</i> (blue plot). <i>D</i> allele has the positive additive effect (green plot; allele effect scale shown on the right) on the expression of <i>Atp5j2</i> and <i>Cplx2</i>; peak LOD scores are on markers near candidate genes <i>Ndufs2</i> and <i>Kcnj10</i>. <i>B</i> allele has the positive additive effect (red plot) on the expression of <i>Nars</i>; peak LOD score is on markers near candidate gene <i>Fmn2</i>. The horizontal lines indicate the genome-wide significant thresholds (<i>p</i>-value = 0.05). Yellow seismograph tracks the SNP density between <i>B</i> and <i>D</i> alleles. Affymetrix probe set ID for each transcript in the BXD hippocampus dataset is shown.</p>", "links"=>[], "tags"=>["genetics and genomics", "genetics and genomics/animal genetics", "genetics and genomics/bioinformatics", "genetics and genomics/complex traits", "genetics and genomics/functional genomics", "genetics and genomics/gene expression", "genetics and genomics/genomics"], "article_id"=>586329, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Segregation_of_trans_QTLs_in_Qrr1_/586329", "title"=>"Segregation of <i>trans</i>-QTLs in <i>Qrr1</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-14 01:45:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/916025"], "description"=>"<p>Transcripts of <i>Gars</i>, <i>Cars</i>, <i>Nars</i>, <i>Mars</i>, and <i>Yars</i> map as <i>trans</i>-QTLs to <i>Qrr1</i> at LOD>4 (genome-wide <i>p</i>-value<0.01) in the BXD hippocampus dataset. The <i>trans</i>-QTLs have peak LOD precisely on markers in distal part of <i>Qrr1</i>, ∼175–177.5 Mb (shaded regions). Yellow seismograph on Chr 1 (x-axis) tracks SNP density between B and D alleles. Affymetrix probe set ID for each transcript is shown.</p>", "links"=>[], "tags"=>["aminoacyl-trna", "synthetases", "distal"], "article_id"=>586477, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_QTL_for_aminoacyl_tRNA_synthetases_in_distal_Qrr1_/586477", "title"=>"QTL for aminoacyl-tRNA synthetases in distal <i>Qrr1</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-14 01:47:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/916107"], "description"=>"<p>SNPs in <i>Qrr1</i> were counted for (A) C57BL/6J (B6)×DBA/2J (D2), (B) B6×BALB/cBy (BALB), (C) B6×C3H/HeJ (C3H), and (D) ILS×ISS. The SNP distribution profiles were generated by plotting the number of SNPs in 250 kb bins. Vertical red lines mark the approximate positions of recombination (corresponds to <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000260#pgen-1000260-g002\" target=\"_blank\">figure 2</a>). Region covered by <i>Qrr1p</i> (horizontal line), candidate genes in <i>Qrr1d</i> (yellow bars), and position of tRNA clusters (triangles) are shown above the graphs. The B6×D2, B6×BALB, and B6×C3H crosses have moderate to high SNP counts throughout <i>Qrr1</i>. In the ILSxISS cross, <i>Qrr1p</i> is relatively SNP-rich but <i>Qrr1d</i> is SNP-sparse.</p>", "links"=>[], "tags"=>["genetics and genomics", "genetics and genomics/animal genetics", "genetics and genomics/bioinformatics", "genetics and genomics/complex traits", "genetics and genomics/functional genomics", "genetics and genomics/gene expression", "genetics and genomics/genomics"], "article_id"=>586557, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNP_comparison_between_crosses_/586557", "title"=>"SNP comparison between crosses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-14 01:49:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/916209"], "description"=>"<p>(A) Neurons exhibited pronounced fine granular immunoreactivity for FMN2. The cell body had the strongest signal. The fine granular staining extended into apical and distal dendrites (arrows). Thin axon-like processes were also labeled (arrow head). (B) The fine granular staining is not detected in controls of sister cultures processed in parallel without the first antibody.</p>", "links"=>[], "tags"=>["fmn2", "hippocampal"], "article_id"=>586660, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_FMN2_protein_in_hippocampal_neurons_/586660", "title"=>"Expression of FMN2 protein in hippocampal neurons.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-14 01:51:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/916332"], "description"=>"<p>Candidate gene <i>Kcnj9</i> (A) has heavy expression in neurons. <i>Kcnj9</i> shows a regionally restricted expression in the hippocampus with intense labeling in dentate gyrus, strong labeling in CA1, and relatively weak labeling in CA2 and CA3. Candidate gene <i>Kcnj10</i> (B) has a more diffused pattern and expressed primarily in glial cells. There is almost no labeling for <i>Kcnj10</i> in the hippocampus. Transcripts of seizure-related genes, <i>Cacna1g</i> (C) and <i>Socs2</i> (D), have trans-QTLs in <i>Qrr1p</i>. Both genes show high expression in neurons. <i>Cacna1g</i> matches the expression of <i>Kcnj9</i> with strong labeling in dentate gyrus and CA1, and weak labeling in CA2 and CA3. <i>Socs2</i> complements the expression of <i>Kcnj9</i> and <i>Cacna1g</i> with intense labeling in CA2 and CA3. <i>In Situ</i> expression data are from the Allen Brain Atlas.</p>", "links"=>[], "tags"=>["patterns", "seizure", "genes"], "article_id"=>586785, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_patterns_of_seizure_related_genes_with_cis_and_trans_QTLs_in_Qrr1p_/586785", "title"=>"Expression patterns of seizure related genes with <i>cis</i>- and <i>trans</i>-QTLs in <i>Qrr1p</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-14 01:53:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/916474"], "description"=>"<p>Classical QTLs on Chr 1 from 172–178 Mb; listed by approximate position from proximal to distal end (adapted from Mouse Genome Informatics).</p>", "links"=>[], "tags"=>["qtls", "chr", "listed", "approximate", "proximal", "distal", "genome"], "article_id"=>586922, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Classical_QTLs_on_Chr_1_from_172_8211_178_Mb_listed_by_approximate_position_from_proximal_to_distal_end_adapted_from_Mouse_Genome_Informatics_/586922", "title"=>"Classical QTLs on Chr 1 from 172–178 Mb; listed by approximate position from proximal to distal end (adapted from Mouse Genome Informatics).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-11-14 01:55:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/916506"], "description"=>"a<p>Number of missense mutations between <i>B</i> and <i>D</i> alleles.</p>b<p>Mean expression signal of probe sets in BXD Hippocampus PDNN dataset; below 7 is considered to be below background.</p>c<p><i>Cis</i>-QTLs in BXD, B6C3HF2, CXB, and LXS crosses.</p>", "links"=>[], "tags"=>["genes"], "article_id"=>586962, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Candidate_genes_in_Qrr1_/586962", "title"=>"Candidate genes in <i>Qrr1</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-11-14 01:56:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/916543"], "description"=>"a<p>Number of RI strains or F2 mice.</p>b<p>Number of <i>cis</i>- and <i>trans</i>-QTLs in <i>Qrr1</i> at minimum LOD of 3; complete list of these transcripts can be retrieved from <a href=\"http://www.genenetwork\" target=\"_blank\">www.genenetwork</a> .org using search key “LRS = (15 500 Chr1 172 178)”.</p>c<p>Percent of <i>trans</i>-QTLs in <i>Qrr1</i> = [(number of <i>trans</i>-QTLs in <i>Qrr1</i>)/(total number of <i>trans</i>-QTLs in the whole genome)×100].</p>d<p>Percent of <i>cis</i>-QTLs in <i>Qrr1</i> = [(number of <i>cis</i>-QTLs in <i>Qrr1</i>)/(total number of <i>cis</i>-QTLs in the whole genome)×100].</p>", "links"=>[], "tags"=>["qtls", "crosses"], "article_id"=>586999, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_QTLs_in_Qrr1_in_different_crosses_and_tissues_/586999", "title"=>"Expression QTLs in <i>Qrr1</i> in different crosses and tissues.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-11-14 01:56:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/916581"], "description"=>"a<p>Probe/Probe set ID.</p>b<p>Physical location of gene; <i>Iars2</i> is located on Chr 1 at 186.9 Mb, and <i>Dars</i> on Chr 1 at 130 Mb.</p>c<p>Dataset in which transcript has highest <i>trans</i>-QTL in <i>Qrr1</i>.</p>d<p>Highest LOD score in <i>Qrr1</i>.</p>e<p>Allele that increases expression.</p>", "links"=>[], "tags"=>["aminoacyl", "trna", "synthetases", "cns"], "article_id"=>587031, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcripts_of_aminoacyl_tRNA_synthetases_that_have_trans_QTLs_in_Qrr1_LOD_3_in_one_or_multiple_CNS_datasets_/587031", "title"=>"Transcripts of aminoacyl tRNA synthetases that have <i>trans</i>-QTLs in <i>Qrr1</i> (LOD≥3) in one or multiple CNS datasets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-11-14 01:57:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/916608"], "description"=>"a<p>Additive effect is computed as [(mean expression in <i>DD</i> homozygote)−(mean expression in <i>BB</i> homozygote)]/2 on a log<sub>2</sub> scale. Positive value means <i>D</i> high expression, and negative value means <i>B</i> high expression.</p>", "links"=>[], "tags"=>["measuring", "allele"], "article_id"=>587062, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_of_cis_QTLs_by_measuring_allele_specific_expression_difference_/587062", "title"=>"Validation of <i>cis</i>-QTLs by measuring allele specific expression difference.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-11-14 01:57:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/916649"], "description"=>"a<p>Illumina probe ID.</p>b<p>Physical location of gene.</p>c<p>Average expression signal in Fmn2-null and wild-type lines.</p>d<p>Fold difference in expression between Fmn2-null and wild-type lines</p>e<p>Bonferroni adjusted <i>p</i>-values; corrected for 46,620 tests.</p>f<p>Highest LOD in <i>Qrr1</i> and dataset in which transcript has highest LOD in <i>Qrr1</i>.</p>", "links"=>[], "tags"=>["genetics and genomics", "genetics and genomics/animal genetics", "genetics and genomics/bioinformatics", "genetics and genomics/complex traits", "genetics and genomics/functional genomics", "genetics and genomics/gene expression", "genetics and genomics/genomics"], "article_id"=>587096, "categories"=>["Genetics"], "users"=>["Khyobeni Mozhui", "Daniel C. Ciobanu", "Thomas Schikorski", "Xusheng Wang", "Lu Lu", "Robert W. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000260.t006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_that_have_significant_expression_difference_between_Fmn2_and_Fmn2_8722_8722_/587096", "title"=>"Genes that have significant expression difference between <i>Fmn2</i><sup>+/+</sup> and <i>Fmn2</i><sup>−/−</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-11-14 01:58:16"}

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Relative Metric

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