Identification of cis-Regulatory Elements in the Mammalian Genome: The cREMaG Database
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{"title"=>"Identification of cis-regulatory elements in the mammalian genome: The cREMaG database", "type"=>"journal", "authors"=>[{"first_name"=>"Marcin", "last_name"=>"Piechota", "scopus_author_id"=>"8574520600"}, {"first_name"=>"Michal", "last_name"=>"Korostynski", "scopus_author_id"=>"55897898600"}, {"first_name"=>"Ryszard", "last_name"=>"Przewlocki", "scopus_author_id"=>"7006034658"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"359771479", "pmid"=>"20824209", "doi"=>"10.1371/journal.pone.0012465", "scopus"=>"2-s2.0-77957955671", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"77957955671", "issn"=>"19326203"}, "id"=>"76f7aad6-3ae2-392b-ba2f-d6e027849709", "abstract"=>"BACKGROUND: A growing number of gene expression-profiling datasets provides a reliable source of information about gene co-expression. In silico analyses of the properties shared among the promoters of co-expressed genes facilitates the identification of transcription factors (TFs) involved in the co-regulation of those genes. Our previous experience with microarray data led to the development of a database suitable for the examination of regulatory motifs in the promoters of co-expressed genes.\\n\\nMETHODOLOGY: We introduce the cREMaG (cis-Regulatory Elements in the Mammalian Genome) system designed for in silico studies of the promoter properties of co-regulated mammalian genes. The cREMaG system offers an analysis of data obtained from human, mouse, rat, bovine and canine gene expression-profiling studies. More than eight analysis parameters can be utilized in user-defined combinations. The selection of alternative transcription start sites and information about CpG islands are also available.\\n\\nCONCLUSIONS: Using the cREMaG system, we successfully identified TFs mediating transcriptional responses in reference gene sets. The cREMaG system facilitates in silico studies of mammalian transcriptional gene regulation. The resource is freely available at http://www.cremag.org.", "link"=>"http://www.mendeley.com/research/identification-cisregulatory-elements-mammalian-genome-cremag-database", "reader_count"=>27, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>12, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Other"=>1, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>12, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Other"=>1, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>23, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}}, "reader_count_by_country"=>{"United States"=>2, "Japan"=>1, "Brazil"=>1, "United Kingdom"=>2, "Chile"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/414705", "https://ndownloader.figshare.com/files/414717", "https://ndownloader.figshare.com/files/414729"], "description"=>"<div><h3>Background</h3><p>A growing number of gene expression-profiling datasets provides a reliable source of information about gene co-expression. <em>In silico</em> analyses of the properties shared among the promoters of co-expressed genes facilitates the identification of transcription factors (TFs) involved in the co-regulation of those genes. Our previous experience with microarray data led to the development of a database suitable for the examination of regulatory motifs in the promoters of co-expressed genes.</p><h3>Methodology</h3><p>We introduce the cREMaG (<em>cis</em>-Regulatory Elements in the Mammalian Genome) system designed for <em>in silico</em> studies of the promoter properties of co-regulated mammalian genes. The cREMaG system offers an analysis of data obtained from human, mouse, rat, bovine and canine gene expression-profiling studies. More than eight analysis parameters can be utilized in user-defined combinations. The selection of alternative transcription start sites and information about CpG islands are also available.</p><h3>Conclusions</h3><p>Using the cREMaG system, we successfully identified TFs mediating transcriptional responses in reference gene sets. The cREMaG system facilitates <em>in silico</em> studies of mammalian transcriptional gene regulation. The resource is freely available at <a href=\"http://www.cremag.org\">http://www.cremag.org</a>.</p></div>", "links"=>[], "tags"=>["elements", "mammalian", "cremag"], "article_id"=>141888, "categories"=>["Genetics", "Cancer", "Biological Sciences"], "users"=>["Marcin Piechota", "Michal Korostynski", "Ryszard Przewlocki"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0012465.s001", "https://dx.doi.org/10.1371/journal.pone.0012465.s002", "https://dx.doi.org/10.1371/journal.pone.0012465.s003"], "stats"=>{"downloads"=>9, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identification_of_cis_Regulatory_Elements_in_the_Mammalian_Genome_The_cREMaG_Database/141888", "title"=>"Identification of <em>cis</em>-Regulatory Elements in the Mammalian Genome: The cREMaG Database", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-08-31 00:31:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/832405"], "description"=>"<p>(A) The view of query step I – the gene-set submission in which the user is asked to input the query name and gene IDs and to select the species, type of Ids and the type of alternative TSSs. (B) The view of query step II – the alternative promoter selection in which the user is asked to confirm the identified genes and alternative promoters. (C) The view of query step III – the user is asked to select the analysis parameters. (D) Query step IV – the results overview. (E) cREMaG visualization of promoters. (F) Detailed table with particular transcription factor binding sites.</p>", "links"=>[], "tags"=>["overview", "graphical"], "article_id"=>502778, "categories"=>["Genetics", "Infectious Diseases", "Virology", "Computational Biology"], "users"=>["Marcin Piechota", "Michal Korostynski", "Ryszard Przewlocki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012465.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_overview_of_the_graphical_user_interface_/502778", "title"=>"An overview of the graphical user interface.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-08-31 00:46:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/832524"], "description"=>"<p>The heatmap plot presents the scores from cREMaG, oPOSSUM, CORE_TF, TFM-Explorer and Pscan for eight selected gene sets. The scores were calculated based on the rank in the results of the expected TFBS matrix: ten points for first rank (dark green color), nine points for second, down to one point for tenth rank (white color). The sum of the scores is presented on the right. The tools and gene sets are ordered by the sum of scores in decreasing order.</p>", "links"=>[], "tags"=>["cremag", "on-line"], "article_id"=>502895, "categories"=>["Genetics", "Infectious Diseases", "Virology", "Computational Biology"], "users"=>["Marcin Piechota", "Michal Korostynski", "Ryszard Przewlocki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012465.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_cREMaG_to_other_on_line_tools_/502895", "title"=>"Comparison of cREMaG to other on-line tools.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-08-31 00:48:15"}

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Relative Metric

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