Leukemia Gene Atlas – A Public Platform for Integrative Exploration of Genome-Wide Molecular Data
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{"title"=>"Leukemia gene atlas - a public platform for integrative exploration of genome-wide molecular data", "type"=>"journal", "authors"=>[{"first_name"=>"Katja", "last_name"=>"Hebestreit", "scopus_author_id"=>"54779897800"}, {"first_name"=>"Sören", "last_name"=>"Gröttrup", "scopus_author_id"=>"55251761500"}, {"first_name"=>"Daniel", "last_name"=>"Emden", "scopus_author_id"=>"55251290600"}, {"first_name"=>"Jannis", "last_name"=>"Veerkamp", "scopus_author_id"=>"55251474800"}, {"first_name"=>"Christian", "last_name"=>"Ruckert", "scopus_author_id"=>"56682214000"}, {"first_name"=>"Hans Ulrich", "last_name"=>"Klein", "scopus_author_id"=>"7403472129"}, {"first_name"=>"Carsten", "last_name"=>"Müller-Tidow", "scopus_author_id"=>"7004555214"}, {"first_name"=>"Martin", "last_name"=>"Dugas", "scopus_author_id"=>"55550317000"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22720055", "sgr"=>"84862255345", "doi"=>"10.1371/journal.pone.0039148", "scopus"=>"2-s2.0-84862255345", "pui"=>"365003249", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"07089ff0-6650-3897-b867-09cfe3a538e7", "abstract"=>"Leukemias are exceptionally well studied at the molecular level and a wealth of high-throughput data has been published. But further utilization of these data by researchers is severely hampered by the lack of accessible integrative tools for viewing and analysis. We developed the Leukemia Gene Atlas (LGA) as a public platform designed to support research and analysis of diverse genomic data published in the field of leukemia. With respect to leukemia research, the LGA is a unique resource with comprehensive search and browse functions. It provides extensive analysis and visualization tools for various types of molecular data. Currently, its database contains data from more than 5,800 leukemia and hematopoiesis samples generated by microarray gene expression, DNA methylation, SNP and next generation sequencing analyses. The LGA allows easy retrieval of large published data sets and thus helps to avoid redundant investigations. It is accessible at www.leukemia-gene-atlas.org.", "link"=>"http://www.mendeley.com/research/leukemia-gene-atlas-public-platform-integrative-exploration-genomewide-molecular-data", "reader_count"=>47, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>5, "Researcher"=>17, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>5, "Researcher"=>17, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>22, "Medicine and Dentistry"=>12, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>12}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "United Kingdom"=>2, "France"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/624053"], "description"=>"<p>Experiment view with information on the integrated study <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039148#pone.0039148-Robinson1\" target=\"_blank\">[15]</a> (above), sample characteristics (hidden, in the middle) and stored result tables (below). Genes with <i>RUNX1</i> binding sites are copied from a table of peak annotations and stored as a gene list. <b>(Middle)</b> Groups of samples from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039148#pone.0039148-Benjamini1\" target=\"_blank\">[14]</a> are defined in the analysis tab. <b>(Below)</b> Selecting the stored gene list (genes with <i>RUNX1</i> binding sites) and performing principle component analysis on the selected groups of samples from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039148#pone.0039148-Benjamini1\" target=\"_blank\">[14]</a>.</p>", "links"=>[], "tags"=>["lga"], "article_id"=>294533, "categories"=>["Biological Sciences", "Hematology"], "users"=>["Katja Hebestreit", "Sören Gröttrup", "Daniel Emden", "Jannis Veerkamp", "Christian Rückert", "Hans-Ulrich Klein", "Carsten Müller-Tidow", "Martin Dugas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039148.g003", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Usage_of_the_LGA_web_interface_Above_/294533", "title"=>"Usage of the LGA web interface. (Above)", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-14 01:15:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/623843"], "description"=>"<p>38 hematopoietic cell populations are shown with their respective positions in hematopoiesis. Cells called as “progenitors” in the analysis are marked by a red box, “non-progenitor” cells are marked by a gray box. Figure adapted from Novershtern et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039148#pone.0039148-Barrett1\" target=\"_blank\">[9]</a>.</p>", "links"=>[], "tags"=>["hematopoietic"], "article_id"=>294326, "categories"=>["Biological Sciences", "Hematology"], "users"=>["Katja Hebestreit", "Sören Gröttrup", "Daniel Emden", "Jannis Veerkamp", "Christian Rückert", "Hans-Ulrich Klein", "Carsten Müller-Tidow", "Martin Dugas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039148.g002", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Populations_of_human_hematopoietic_cells_/294326", "title"=>"Populations of human hematopoietic cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-14 01:12:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/623736"], "description"=>"<p>Data is imported from several online repositories and the medical literature into the LGA database. An analysis module processes the molecular data. The application server handles data transfer between database and analysis module and can be accessed through a web interface. It executes queries and forwards data and analysis results to the client.</p>", "links"=>[], "tags"=>["lga"], "article_id"=>294215, "categories"=>["Biological Sciences", "Hematology"], "users"=>["Katja Hebestreit", "Sören Gröttrup", "Daniel Emden", "Jannis Veerkamp", "Christian Rückert", "Hans-Ulrich Klein", "Carsten Müller-Tidow", "Martin Dugas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039148.g001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_the_LGA_architecture_/294215", "title"=>"Overview of the LGA architecture.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-14 01:10:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/624316"], "description"=>"<p>Overview of data in the LGA.</p>", "links"=>[], "tags"=>["Computational biology", "hematology"], "article_id"=>294793, "categories"=>["Biological Sciences", "Hematology"], "users"=>["Katja Hebestreit", "Sören Gröttrup", "Daniel Emden", "Jannis Veerkamp", "Christian Rückert", "Hans-Ulrich Klein", "Carsten Müller-Tidow", "Martin Dugas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039148.t001", "stats"=>{"downloads"=>6, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_data_in_the_LGA_/294793", "title"=>"Overview of data in the LGA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-14 01:19:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/323656", "https://ndownloader.figshare.com/files/323693"], "description"=>"<div><p>Leukemias are exceptionally well studied at the molecular level and a wealth of high-throughput data has been published. But further utilization of these data by researchers is severely hampered by the lack of accessible integrative tools for viewing and analysis. We developed the Leukemia Gene Atlas (LGA) as a public platform designed to support research and analysis of diverse genomic data published in the field of leukemia. With respect to leukemia research, the LGA is a unique resource with comprehensive search and browse functions. It provides extensive analysis and visualization tools for various types of molecular data. Currently, its database contains data from more than 5,800 leukemia and hematopoiesis samples generated by microarray gene expression, DNA methylation, SNP and next generation sequencing analyses. The LGA allows easy retrieval of large published data sets and thus helps to avoid redundant investigations. It is accessible at <a href=\"http://www.leukemia-gene-atlas.org\">www.leukemia-gene-atlas.org</a>.</p> </div>", "links"=>[], "tags"=>["leukemia", "atlas", "integrative", "genome-wide", "molecular"], "article_id"=>123882, "categories"=>["Biological Sciences", "Hematology"], "users"=>["Katja Hebestreit", "Sören Gröttrup", "Daniel Emden", "Jannis Veerkamp", "Christian Rückert", "Hans-Ulrich Klein", "Carsten Müller-Tidow", "Martin Dugas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039148.s001", "https://dx.doi.org/10.1371/journal.pone.0039148.s002"], "stats"=>{"downloads"=>2, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Leukemia_Gene_Atlas_A_Public_Platform_for_Integrative_Exploration_of_Genome_Wide_Molecular_Data/123882", "title"=>"Leukemia Gene Atlas – A Public Platform for Integrative Exploration of Genome-Wide Molecular Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-06-14 01:04:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/624187"], "description"=>"<p>(<b>A</b>) Screenshot of a t-test result table with the 33 most differentially expressed genes with <i>RUNX1</i> binding sites in progenitor and non-progenitor cells. (<b>B</b>) Distribution of <i>RUNX1</i> expression for different leukemic disease states. (<b>C</b>) Heat map and hierarchical clustering of patients with acute lymphoblastic leukemia and non-leukemia samples with healthy bone marrows for gene expression of genes with RUNX1 binding sites and highest variances over all samples. The phenotype color grid at the top represents the sample characteristics. (<b>D</b>) Kaplan Meier curves of event-free survival for patients with acute myeloid leukemia with low (≤33% quantile), median (>33% quantile and ≤66% quantile), and high <i>RUNX1</i> expression (>66% quantile).</p>", "links"=>[], "tags"=>["binding", "sites"], "article_id"=>294669, "categories"=>["Biological Sciences", "Hematology"], "users"=>["Katja Hebestreit", "Sören Gröttrup", "Daniel Emden", "Jannis Veerkamp", "Christian Rückert", "Hans-Ulrich Klein", "Carsten Müller-Tidow", "Martin Dugas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039148.g004", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_role_of_RUNX1_and_its_binding_sites_in_leukemias_/294669", "title"=>"The role of <i>RUNX1</i> and its binding sites in leukemias.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-14 01:17:49"}

PMC Usage Stats | Further Information

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Relative Metric

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