In-silico human genomics with GeneCards
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In-silico human genomics with GeneCards Gil Stelzer,1* Irina Dalah,1 Tsippi Iny Stein,1 Yigeal Satanower,1 Naomi Rosen,1 Noam Nativ,1 Danit Oz-Levi,1 Tsviya Olender,1 Frida Belinky,1 Iris Bahir,1 Hagit Krug,1 Paul Perco,2 Bernd Mayer,3 Eugene Kolker,4 Marilyn Safran1,5 and Doron Lancet1 1
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel Emergentec Biodevelopment GmbH, Vienna, Austria 3 Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria 4 Seattle Children’s Research Institute at the Seattle Children’s Hospital, and Informatics Department, School of Medicine, University of Washington, Seattle, WA 98101, USA 5 Department of Biological Services, Weizmann Institute of Science, Rehovot, 76100, Israel *Correspondence to: Tel: þ1 9728 934 4406; Fax: þ1 9728 934 4487; E-mail: [email protected] 2
Date received (in revised form): 23 May 2011
Abstract Since 1998, the bioinformatics, systems biology, genomics and medical communities have enjoyed a synergistic relationship with the GeneCards database of human genes (http://www.genecards.org). This human gene compendium was created to help to introduce order into the increasing chaos of information flow. As a consequence of viewing details and deep links related to specific genes, users have often requested enhanced capabilities, such that, over time, GeneCards has blossomed into a suite of tools (including GeneDecks, GeneALaCart, GeneLoc, GeneNote and GeneAnnot) for a variety of analyses of both single human genes and sets thereof. In this paper, we focus on inhouse and external research activities which have been enabled, enhanced, complemented and, in some cases, motivated by GeneCards. In turn, such interactions have often inspired and propelled improvements in GeneCards. We describe here the evolution and architecture of this project, including examples of synergistic applications in diverse areas such as synthetic lethality in cancer, the annotation of genetic variations in disease, omics integration in a systems biology approach to kidney disease, and bioinformatics tools. Keywords: GeneCards, GeneDecks, Partner Hunter, Set Distiller, omics, genomics, human genes, database, synthetic lethality, genetic variations
GeneCards system evolution and architecture From the very beginning, the core GeneCards features included two important components: the capability to view integrated details about a gene in ‘card’ format and a full text-based search engine. GeneCards has evolved by constantly adding new data sources and data types (eg protein expression and gene networks), revamping the search engine to improve results and performance, and expanding the original gene-centric dogma to encompass sets of genes.
Currently, GeneCards automatically mines over 90 sources in an offline process and constructs a consolidated gene list. First, the complete current snapshot of the HUGO Gene Nomenclature Committee (HGNC)-approved symbols1 is used as the core gene list. Next, human Entrez Gene2 entries that are differe
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