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Open Access Genome databases

In-silico human genomics with GeneCards

Gil Stelzer1*, Irina Dalah1, Tsippi Iny Stein1, Yigeal Satanower1, Naomi Rosen1, Noam Nativ1, Danit Oz-Levi1, Tsviya Olender1, Frida Belinky1, Iris Bahir1, Hagit Krug1, Paul Perco2, Bernd Mayer3, Eugene Kolker4, Marilyn Safran15 and Doron Lancet1

Author Affiliations

1 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel

2 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

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Human Genomics 2011, 5:709-717  doi:10.1186/1479-7364-5-6-709

Published: 1 October 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 webcite). 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