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Discovering Interactions and Connections with Bioinformatics Tools at RGD
Author(s) -
Shimoyama Mary,
Laulederkind Stanley,
De Pons Jeff,
Tutaj Marek,
Thota Jyothi,
Ghiasvand Omid,
Petri Victoria,
Smith Jennifer R,
Hayman G. Thomas,
Wang ShurJen,
Dwinell Melinda
Publication year - 2017
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.31.1_supplement.722.9
Subject(s) - computer science , upload , genome browser , ontology , variety (cybernetics) , genome , function (biology) , information retrieval , data mining , computational biology , genomics , gene , world wide web , biology , genetics , artificial intelligence , philosophy , epistemology
The bioinformatics platform at the Rat Genome Database (RGD) (rgd.mcw.edu) provides researchers with multiple tools to identify and analyze interactions and connections among genomic elements for rat, human, and mouse. These tools allow investigators to create complex queries to retrieve genomic elements of interest, add to or filter these elements by a variety of parameters and analyze the resulting data subsets. Navigation among tools is seamless without the need to re‐format or re‐enter data to be analyzed. OLGA (Object List Generator & Analyzer) and the Ontology Browser allow users to retrieve rat, human, or mouse genes, or rat QTL and strains by categories found in multiple ontologies for gene function, biological process, cellular component, pathway, disease, phenotype, chemical/drug‐gene interaction. In addition, OLGA allows users to search by genomic region, QTL region or upload a symbol list of their own. OLGA provides functions for creating additional data element lists using any of the search functions and then allowing the user to create a union or intersection of the lists or to subtract one list from the other. This provides researchers with the ability to create multiple gene lists, for example, based on multiple parameters and create larger datasets or smaller subsets in an easy manner. Investigators can send the results of either the OLGA or Ontology Browser searches to a variety of tools with a single click. Genomic elements can be visualized across the entire genome via the Genome Viewer, which then allows users to overlap additional data for pathways, QTL, or other gene lists. Comprehensive reports for each gene in a list can be easily retrieved from the Gene Annotator tool with a single click along with data for orthologs. Other functions of the GA Tool are also available with a single click including the HeatMap and the Annotation Distribution tools which allow the user to further investigate functional similarities within their dataset and identify additional subsets of interest. Protein‐Protein Interactions for all of the genes within the list are also retrieved with a single click on the InterViewer tool. Equally easily, a quick visualization of any damaging variants found in over 40 strains sequenced is available as well as access to the Variant Visualizer for comprehensive filtering and visualization of gene variants. Data downloads are also available. RGD provides a comprehensive bioinformatics platform for rat, human, and mouse data that allows users to easily retrieve customized datasets for analysis and visualization using a bank of innovative tools. Support or Funding Information HL64541 from the National Heart, Lung and Blood Institute on behalf of the NIHOLGA tool with search results for blood coagulation disease genes and genes that interact with Warfarin and options for analysisHeatmap showing a subset of blood coagulation genes that interact with Warfarin and also are associated with heart diseases and an innate immune response pathway