GeneCards- genome-wide gene and disease databases
For over 15 years, we have developed and expanded GeneCards (www.genecards.org ) a comprehensive, authoritative compendium of annotative information about human genes, widely used worldwide. Its gene-centric content is automatically mined and integrated from over 100 electronic sources, resulting in a web-based deep-linked card for each of more than 100,000 human gene entries. GeneCards and its associated suite of bioinformatics tools also feature a highly effective search of all mined data; links to gene-related research reagents such as antibodies, recombinant proteins, DNA clones and inhibitory RNAs; the GeneALaCart batch query engine for annotative information on set of genes; GeneDecks, a systems biology facility, which leverages GeneCards’ unique wealth of combinatorial annotations, via its Partner Hunter for finding “more genes like me”, and Set Distiller for discerning enriched descriptors in sets of genes. Two major recent research focuses include the expansion of RNA genes within GeneCards, and the introduction of a new disease-centric database called MalaCards (Figure).
Figure: MalaCards - a database of human diseases. Malacards ( http://www.malacards.org) integrates many heterogeneous, incomplete, non-standardized malady sources. For each human disease, MalaCards provides a computerized web card, with prioritized annotative information, leveraging the richness of GeneCards.
The realm of ncRNA (non protein-coding RNA) gene databases is a complex network of mutually linked data structures. The integration effort allows to judiciously unify all ncRNA entries obtainable from 15 different primary sources, resulting in >50,000 RNA genes within GeneCards, a three-fold increase over previous versions. Moving from gene-centric to disease-centric, we’ve also introduced a new integrated searchable database of human diseases and their annotations, called MalaCards (www.malacards.org), which tackles the labyrinth of heterogeneous, inconsistent, on-line medical data, consolidates information from 33 sources, resulting in the inclusion of >15,000 disease cards. MalaCards exploits GeneCards/GeneDecks annotations and relationships to present a web card for each of these diseases, containing knowledge knowledge in the realms of disease aliases, descriptions and summaries, related diseases, anatomical context, clinical features, publications, genetic tests, drugs and therapeutics. MalaCards also shows comprehensive relationships of each disease to genes and their annotations, such as pathways, go terms and expression patterns, . GeneCards and MalaCards play a key role in numerous projects for identifying mutations and SNPs underlying genetic, rare, and complex diseases.
• Belinky, F., Bahir, I., Stelzer, G., Rosen, N., Nativ, N., Rappaport, N., Dalah, I., Iny Stein, T., Mituyama, T., Safran, M. and Lancet, D. Non-redundant compendium of human ncRNA genes in GeneCards. Bioinformatics (in press)
• Kolker E., Higdon R., Haynes W., Welch D., Broomall W., Lancet D., Stanberry L. and Kolker N. MOPED: Model Organism Protein Expression Database. Nucleic Acids Res. Jan;40(Database issue):D1093-9. Epub 2011 Dec 1 (2012).
• 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, Aug 5: baq020 (2010)
• Stelzer,G., Inger, A., Olender, T., Iny-Stein, T., Dalah, I., Harel, A., Safran, M. and Lancet, D. GeneDecks: paralog hunting and gene-set distillation with GeneCard annotation. OMICS 13 (6):477-87 (2009)
• Harel,A., Inger,A., Stelzer, G., Strichman-Almashanu, l., Dalah, I.,Safran, M. And Lancet, D. GIFtS: annotation landscape analysis with GeneCards. BMC Bioinformatics, 10:348 (2009).
• Ferrari, F., Bortoluzzi, S., Coppe, A., Sirota, A., Safran, M., Ferrari, S., Lancet, D., Danieli, G.A., Biccatio, S.:Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics. 15; 8:446-453. (2007).
• Yanai, I., Benjamin, H., Shmoish, M., Chalifa-Caspi, V., Shklar, M., Ophir, R., Bar-Even, A., Horn-Saban, S., Safran, M., Domany, E., Lancet, D. and Shmueli, O. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21(5):650-659 (2005).
• Shklar, M., Strichman-Almashanu, L., Shmueli, O., Shmoish, M., Safran, M. and Lancet, D. GeneTide – Terra Incognita Discovery Endeavor: A new transcriptome focused member of the GeneCards/GeneNote suite of databases. Nucleic Acids Res. 33:D556-561 (2005).
• Chalifa-Caspi, V., Yanai, I., Ophir, R., Rosen, N., Shmoish, M., Benjamin-Rodrig, H., Iny Stein, T., Shmueli, O., Safran, M. and Lancet, D. GeneAnnot: Comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes. Bioinformatics 20(9):1457-1458 (2004).
• Rosen, N., Chalifa-Caspi, V., Shmueli, O., Adato, A., Lapidot, M., Stampnitzky, J., Safran, M. and Lancet, D. GeneLoc: Exon-based integration of human genome maps. Bioinformatics (ISMB). 19(1): 1222-1224 (2003).
• Safran, M., Solomon, I., Shmueli, O., Lapidot, M., Shen-Orr, S., Adato, A., Ben-Dor, U., Esterman, N., Rosen, N., Peter, I., Olender, T., Chalifa-Caspi, V. and Lancet, D. GeneCardsTM 2002: Towards a complete, object-oriented, human gene compendium. Bioinformatics, 18(11): 1542-1543 (2002).
• Rebhan, M., Chalifa-Caspi, V., Prilusky, J. and Lancet, D. GeneCards : A novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics 14(8): 656-664 (1998).
• Rebhan, M., Chalifa-Caspi, V., Prilusky, J. and Lancet, D. GeneCards: Integrating Information about Genes, Proteins and Diseases. Trends in Genetics 13(4): 163 (1997).
Reviews and Book Chapters
• Chalifa-Caspi, V., Shmueli, O., Benjamin-Rodrig, H., Rosen, N., Shmoish, M., Yanai, I., Ophir, R., Kats, P., Safran, M. and Lancet, D. GeneAnnot: Interfacing GeneCards with high throughput gene expression compendia. Brief Bioinform. 4(4):349-60 (2003).
• Stelzer, G., Dalah, I., Iny Stein, T., Rosen, N., Nativ, N., Krug H., Oz-Levi, D., Olender, T., Belinky, F., Satanower, Y., Bahir, I., Perco, P., Mayer, B., Safran, M. and Lancet, D. In-silico Human Genomics with GeneCards. Human Genomics, 5(6) 709–717 (2011).
• Shmueli, O., Horn-Saban, S., Chalifa-Caspi, V., Shmoish, M., Ophir, R., Benjamin-Rodrig, H., Safran, M., Domany, E. and Lancet, D. GeneNoTe: whole genome expression profiles in normal human tissues. Comptes Rendus Biologies de L'Academie des Sciences, Life Sciences 326: 1067-1072 (2003).