Quantitative Expression Profile of Distinct Functional Regions in the Adult Mouse Brain
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{"title"=>"Quantitative expression profile of distinct functional regions in the adult mouse brain", "type"=>"journal", "authors"=>[{"first_name"=>"Takeya", "last_name"=>"Kasukawa", "scopus_author_id"=>"6603860842"}, {"first_name"=>"Koh hei", "last_name"=>"Masumoto", "scopus_author_id"=>"7006574224"}, {"first_name"=>"Itoshi", "last_name"=>"Nikaido", "scopus_author_id"=>"6602838205"}, {"first_name"=>"Mamoru", "last_name"=>"Nagano", "scopus_author_id"=>"7202901652"}, {"first_name"=>"Kenichiro D.", "last_name"=>"Uno", "scopus_author_id"=>"12801068100"}, {"first_name"=>"Kaori", "last_name"=>"Tsujino", "scopus_author_id"=>"37094097700"}, {"first_name"=>"Carina", "last_name"=>"Hanashima", "scopus_author_id"=>"6507792639"}, {"first_name"=>"Yasufumi", "last_name"=>"Shigeyoshi", "scopus_author_id"=>"6603784123"}, {"first_name"=>"Hiroki R.", "last_name"=>"Ueda", "scopus_author_id"=>"56259345600"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-80051622718", "pui"=>"362336065", "doi"=>"10.1371/journal.pone.0023228", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"80051622718", "pmid"=>"21858037"}, "id"=>"2537dc56-2513-38a9-9632-4dc331848126", "abstract"=>"The adult mammalian brain is composed of distinct regions with specialized roles including regulation of circadian clocks, feeding, sleep/awake, and seasonal rhythms. To find quantitative differences of expression among such various brain regions, we conducted the BrainStars (B*) project, in which we profiled the genome-wide expression of ∼50 small brain regions, including sensory centers, and centers for motion, time, memory, fear, and feeding. To avoid confounds from temporal differences in gene expression, we sampled each region every 4 hours for 24 hours, and pooled the samples for DNA-microarray assays. Therefore, we focused on spatial differences in gene expression. We used informatics to identify candidate genes with expression changes showing high or low expression in specific regions. We also identified candidate genes with stable expression across brain regions that can be used as new internal control genes, and ligand-receptor interactions of neurohormones and neurotransmitters. Through these analyses, we found 8,159 multi-state genes, 2,212 regional marker gene candidates for 44 small brain regions, 915 internal control gene candidates, and 23,864 inferred ligand-receptor interactions. We also found that these sets include well-known genes as well as novel candidate genes that might be related to specific functions in brain regions. We used our findings to develop an integrated database (http://brainstars.org/) for exploring genome-wide expression in the adult mouse brain, and have made this database openly accessible. These new resources will help accelerate the functional analysis of the mammalian brain and the elucidation of its regulatory network systems.", "link"=>"http://www.mendeley.com/research/quantitative-expression-profile-distinct-functional-regions-adult-mouse-brain-5", "reader_count"=>5, "reader_count_by_academic_status"=>{"Researcher"=>2, "Student > Ph. D. Student"=>2, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Researcher"=>2, "Student > Ph. D. Student"=>2, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Agricultural and Biological Sciences"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Unspecified"=>1, "Neuroscience"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "group_count"=>0}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/745923"], "description"=>"<p>(<b>A</b>) Map of 44 of the 51 sampled CNS regions. The other seven regions are listed. (<b>B</b>) Abbreviations and full names of CNS regions. (<b>C</b>) Hierarchical clusters of the expression profiles of the 51 CNS regions. Background colors indicate the classical developmental/evolutional/anatomical classification of each region.</p>", "links"=>[], "tags"=>["cns"], "article_id"=>416291, "categories"=>["Biological Sciences", "Neuroscience", "Genetics"], "users"=>["Takeya Kasukawa", "Koh-hei Masumoto", "Itoshi Nikaido", "Mamoru Nagano", "Kenichiro D. Uno", "Kaori Tsujino", "Carina Hanashima", "Yasufumi Shigeyoshi", "Hiroki R. Ueda"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0023228.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampled_adult_mouse_CNS_regions_/416291", "title"=>"Sampled adult mouse CNS regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-12 01:44:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/746045"], "description"=>"<p>(<b>A</b>) Histogram giving the number of different states observed for the 45,037 non-control probe sets. (<b>B</b>) CNS regions that tended to be selected repeatedly as having “up” states of multi-state genes in various gene categories. Rows represent gene categories, and columns represent CNS regions. Asterisks indicate that the number of genes was significantly enriched in the designated CNS region (Bonferroni corrected <i>P</i>-value <0.05). (<b>C</b>) Examples of one-state, two-state, three-state, and four-state genes. Upper graphs show the expression values in 48 CNS regions, and lower graphs are histograms of the expression values and fitted Gaussian mixture models. The order of CNS regions in the expression graphs is the same as shown in <b>Figure 2B</b>. States are distinguished by color. (<b>D</b>) Examples of GPCR genes with multi-state spatial expression patterns. The order of CNS regions in the expression graph is the same as shown in <b>Figure 2B</b>.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "neuroscience"], "article_id"=>416410, "categories"=>["Biological Sciences", "Neuroscience", "Genetics"], "users"=>["Takeya Kasukawa", "Koh-hei Masumoto", "Itoshi Nikaido", "Mamoru Nagano", "Kenichiro D. Uno", "Kaori Tsujino", "Carina Hanashima", "Yasufumi Shigeyoshi", "Hiroki R. Ueda"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0023228.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multi_state_genes_/416410", "title"=>"Multi-state genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-12 01:46:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/746149"], "description"=>"<p>(<b>A</b>) Heat maps of the expressions of marker gene candidates. Genes expressed at higher (left-lower) or lower (right-lower) levels in single regions are shown. The columns of the heat maps represent CNS regions whose order is shown at the left top of this panel. (<b>B</b>) GeneChip expression profiles (upper) of six marker gene candidates: <i>Dsp</i> (highly expressed in the DG), <i>Il1r1</i> (DG), <i>Gpr151</i> (Hb), <i>Chrnb4</i> (Hb), <i>Hcrt</i> (DM), and <i>Npvf</i> (DM) were also confirmed to be expressed in the corresponding regions by <i>in situ</i> hybridization (lower). Inferred states of marker gene candidates are distinguished by color in the upper charts. The order of CNS regions in the expression graphs is the same as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023228#pone-0023228-g002\" target=\"_blank\"><b>Figure 2B</b></a>.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "neuroscience"], "article_id"=>416517, "categories"=>["Biological Sciences", "Neuroscience", "Genetics"], "users"=>["Takeya Kasukawa", "Koh-hei Masumoto", "Itoshi Nikaido", "Mamoru Nagano", "Kenichiro D. Uno", "Kaori Tsujino", "Carina Hanashima", "Yasufumi Shigeyoshi", "Hiroki R. Ueda"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0023228.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regional_marker_gene_candidates_/416517", "title"=>"Regional marker gene candidates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-12 01:48:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/746265"], "description"=>"<p>(<b>A</b>) One-state genes with the 50 most stable (left panel) and variable (right panel) expression patterns. Each box shows the 0.25- to 0.75-quantiles of expression levels in 48 CNS regions for each probe set, and the error bars show the range of expression for all 48 regions. (<b>B</b>) Expression graphs for nine stable one-state genes identified in this study and three well-known internal control genes (<i>Gapdh</i>, <i>Actb</i>, and <i>Tbp</i>, right). The order of CNS regions in the expression graphs is the same as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023228#pone-0023228-g002\" target=\"_blank\"><b>Figure 2B</b></a>. Top row, genes for metabolic process proteins. Middle row, genes for structural proteins. Bottom row, genes for transcription factors, expressed at high (left), intermediate (middle), and low (right) levels.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "neuroscience"], "article_id"=>416631, "categories"=>["Biological Sciences", "Neuroscience", "Genetics"], "users"=>["Takeya Kasukawa", "Koh-hei Masumoto", "Itoshi Nikaido", "Mamoru Nagano", "Kenichiro D. Uno", "Kaori Tsujino", "Carina Hanashima", "Yasufumi Shigeyoshi", "Hiroki R. Ueda"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0023228.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Internal_control_genes_/416631", "title"=>"Internal control genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-12 01:50:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/746393"], "description"=>"<p>(<b>A</b>) Pairs of CNS regions that tended to express the ligand gene for a neurohormone (NH) or neurotransmitter (NT) in one region and its cognate receptor gene in the other. The color of each tile represents the number of ligand-receptor pairs that had “up” states in the corresponding pair of CNS regions. (<b>B</b>) Graphical representation of the putative connections among CNS regions. Arrows originate in the ligand-expressing region and point to the region expressing the cognate NH/NT receptors, when >17 (0.05 quantile of the distribution of all combinations of regions) ligand–receptor pairs were expressed in the two regions. (<b>C</b>–<b>F</b>) Examples of inferred intrinsic ligand-receptor connections. (<b>G</b>) Examples of inferred extrinsic connections. The order of CNS regions in the expression graphs is as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023228#pone-0023228-g002\" target=\"_blank\"><b>Figure 2B</b></a>.</p>", "links"=>[], "tags"=>["connections", "cns"], "article_id"=>416761, "categories"=>["Biological Sciences", "Neuroscience", "Genetics"], "users"=>["Takeya Kasukawa", "Koh-hei Masumoto", "Itoshi Nikaido", "Mamoru Nagano", "Kenichiro D. Uno", "Kaori Tsujino", "Carina Hanashima", "Yasufumi Shigeyoshi", "Hiroki R. Ueda"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0023228.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inferred_connections_among_CNS_regions_/416761", "title"=>"Inferred connections among CNS regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-12 01:52:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/746514"], "description"=>"<p>(<b>A</b>) Scatter plots comparing the BrainStars expression datasets with the BioGPS (top-left), Teragenomics (top-right), and Allen Brain Atlas (ABA) expression level (bottom-left) datasets. All expression values were log<sub>2</sub>-transformed. (<b>B</b>) Summary of the comparison of our marker gene candidates with ABA. Our 120 marker gene candidates with corresponding entries in the target dataset were classified as “matched”, “mismatched”, “unconfirmable”, or “N/A (not available)”. (<b>C</b>) Heatmaps of 120 marker gene candidates in the BrainStars, and ABA datasets. (<b>D</b>) The BrainStars, and ABA expression data for three marker gene candidates: <i>Foxb1</i>, <i>Peg10</i>, and <i>Tcfap2d</i>, show, respectively, agreement in datasets, or a lack of agreement between the datasets. For each gene, the BrainStars expression values were mapped onto slice images and are also represented as bar graphs, and the ABA <i>in situ</i> images are shown. The order of CNS regions in the expression graphs is as in <b>Figure 6C</b>. PVA: paraventricular thalamic nucleus, anterior part. Gi: gigantocellular reticular nucleus.</p>", "links"=>[], "tags"=>["brainstars", "dataset"], "article_id"=>416880, "categories"=>["Biological Sciences", "Neuroscience", "Genetics"], "users"=>["Takeya Kasukawa", "Koh-hei Masumoto", "Itoshi Nikaido", "Mamoru Nagano", "Kenichiro D. Uno", "Kaori Tsujino", "Carina Hanashima", "Yasufumi Shigeyoshi", "Hiroki R. Ueda"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0023228.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_BrainStars_dataset_with_other_resources_/416880", "title"=>"Comparison of BrainStars dataset with other resources.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-12 01:54:40"}

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Relative Metric

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