Close Up - group of the month
SysKid Close up: Let’s meet P19-WEIZMANN (Weizmann Institute of Science)
GeneCards
In the midst of the “Genome Project”, and with the expected onslaught of follow-up data, GeneCards (www.genecards.org) was founded in 1996 at the Weizmann Institute of Science to serve as “the human gene integrator”, with the capacity to integrate data from various sources, and present it in a gene-centric fashion. The GeneCards human gene database extracts and integrates a carefully selected subset of gene-related transcriptomic, genetic, proteomic, functional and disease information, from dozens of relevant sources. It provides robust user-friendly access to up-to-date knowledge. GeneCards overcomes barriers of data format heterogeneity, and uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each gene, and provides the means to obtain a deep understanding of biology and medicine. Information is organized in 20 GeneCards sections, including Drugs and Compounds/Metabolites and the Variations section which provides SNP accessions and CNV data. Where available, links to gene-related products appear alongside scientific annotations, which caters to a diverse user base, including in-vivo, in-vitro, and in-silico academic researchers, clinicians, and biotech companies. One of GeneCards’ major strengths is that it creates order in gene nomenclature, by consolidating multiple aliases and descriptions provided by various data sources. By querying its robust search engine, users can rapidly identify genes of interest by various identifiers and keywords, and pinpoint hits via a relevant and compact “Minicard” search result format. Moving from one gene to many, GeneDecks, which is a part of the GeneCards suite, can identify similar genes with shared annotations, as well as distill descriptors common to sets of genes.
The Genome Center
The Crown Human Genome Center, established in 1997 at the Weizmann Institute of Science, with support from the Israel Ministry of Science, has enabled scientists at the Institute and throughout Israel to investigate new scientific challenges that lie beyond the initial mapping of the human genome. Among its various activities, the center offers consultation and practical help in gene mapping, genotyping, database searching, and genomic sequencing. In addition to next generation deep sequencing, the Center has introduced high-throughput SNP instruments, robots for DNA preparations and labeling reactions and microsatellite mapping, DNA array spotters and scanners, and hardware and software for computational genomics. High-throughput studies supported by the Center include, amongst others, microRNA analysis in Lou Gehrig's disease patients, investigations of the adaptive immune system at work in bacteria with a potential to develop new antibiotics, and examination of the genetics of a variety of monogenic and polygenic diseases. The monogenic conditions, such as a rare form of microcephaly, or a devastating, inherited form of infant diarrhea, offer opportunities to understand the effects of a single genetic variation of a single gene associated with the disease. Other ongoing projects include examining the genetics of Jewish families with multiple cases of schizophrenia, and genetic variations leading to differences in smelling phenotypes. The genome center’s cumulative experience with deciphering connections between complex diseases and the genes that cause them provide a foundation for helping us understand some of the mechanisms that drive the development of Chronic Kidney Disease.
GeneCards and SysKid
Systems biology is a mechanism for enabling scientific conclusions based on broad-scoped findings. We are at a central point in the SysKid research, aiming to draw “big picture” inferences by intersecting data originating from diverse disciplines, such as metabolomics, proteomics and transcriptomics. We are in the process of building a sophisticated integrated database to support disease investigation, where the underlying mechanisms are intricate, as in Chronic Kidney Disease. In addition, this important collaboration could catalyze the development of new tools for analyzing and viewing this information. Furthermore, since the number of genes is rising constantly, most of which are non-coding RNA genes, the challenge of understanding their role in complex diseases, such as CKD, could advance their elucidation.
GeneCards and Genome Center Teams
The GeneCards team includes bioinformaticians and software engineers. Those who work on SysKid related topics are -
Gil Stelzer
Gil holds a PhD in molecular biology, and is currently a research staff scientist. His main responsibilities include GeneDecks and SysKid applications (mainly GeneKid).
Frida Belinky
Frida holds a PhD in bioinformatics, and is currently a Postdoc focusing on RNA genes and orthology.
Iris Bahir
Iris holds a PhD in bioinformatics, and is also a medical student. She is currently focused on RNA genes (piRNAs).
Marilyn Safran
Marilyn holds an MSc in computer science. She is the head of GeneCards development, and liaison with our business partner (Xennex) and customers.
Crown Human Genome Center staff scientists include –
Tsviya Olender
Tsviya holds a PhD in chemistry, and is the Center’s bioinformatician.
Edna Ben-Asher
Edna holds a PhD in molecular genetics, and is the manager of the Crown Genome Center projects.
Doron Lancet
Holds a PhD in chemistry, and is the Principal Investigator of our research group with four major investigation interests: origin of life, hereditary diseases, olfaction and GeneCards, and is the director of the Crown Human Genome Center
Selected References
Stelzer, G., Dalah, I., Iny Stein, T., Satanower, Y., Rosen, N., Nativ, N., Oz-Levi, D., Olender, T., Belinky, F., Bahir, I., Krug, H., Perco, P., Mayer, B., Kolker, E., Safran, M., and Lancet, D. In-silico Human Genomics with GeneCards, Human Genomics (in press)
Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, Nativ N, Bahir I, Doniger T, Krug H, Sirota-Madi A, Olender T, Golan Y, Stelzer G, Harel A, Lancet D. GeneCards Version 3: the human gene integrator. Database (Oxford). 2010 :baq020.
Stelzer G, Inger A, Olender T, Iny-Stein T, Dalah I, Harel A, Safran M, Lancet D. GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation. OMICS. 2009 13(6):477-87.
Rebhan, M., Chalifa-Caspi, V., Prilusky, J., Lancet, D. GeneCards: integrating information about genes, proteins and diseases. Trends in Genetics 13: 163 (1997)
