The DOI matches its Crossref record; 18 of the 18 references it cites were found in a registry or an index.
GeneCards Version 3: the human gene integrator
Open accessAbstract
GeneCards (www.genecards.org) is a comprehensive, authoritative compendium of annotative information about human genes, widely used for nearly 15 years. Its gene-centric content is automatically mined and integrated from over 80 digital sources, resulting in a web-based deep-linked card for each of >73,000 human gene entries, encompassing the following categories: protein coding, pseudogene, RNA gene, genetic locus, cluster and uncategorized. We now introduce GeneCards Version 3, featuring a speedy and sophisticated search engine and a revamped, technologically enabling infrastructure, catering to the expanding needs of biomedical researchers. A key focus is on gene-set analyses, which leverage GeneCards' unique wealth of combinatorial annotations. These include the GeneALaCart batch query facility, which tabulates user-selected annotations for multiple genes and GeneDecks, which identifies similar genes with shared annotations, and finds set-shared annotations by descriptor enrichment analysis. Such set-centric features address a host of applications, including microarray data analysis, cross-database annotation mapping and gene-disorder associations for drug targeting. We highlight the new Version 3 database architecture, its multi-faceted search engine, and its semi-automated quality assurance system. Data enhancements include an expanded visualization of gene expression patterns in normal and cancer tissues, an integrated alternative splicing pattern display, and augmented multi-source SNPs and pathways sections. GeneCards now provides direct links to gene-related research reagents such as antibodies, recombinant proteins, DNA clones and inhibitory RNAs and features gene-related drugs and compounds lists. We also portray the GeneCards Inferred Functionality Score annotation landscape tool for scoring a gene's functional information status. Finally, we delineate examples of applications and collaborations that have benefited from the GeneCards suite. Database URL: www.genecards.org.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232
The Universal Protein Resource (UniProt)
Bairoch, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki070 · Cited by 3,774
A gene atlas of the mouse and human protein-encoding transcriptomes
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400782101 · Cited by 3,475
MINT: the Molecular INTeraction database
Chatr-aryamontri, A., Ceol, A., Palazzi, L. M., Nardelli, G., Schneider, M. V., Castagnoli, L., & Cesareni, G. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl950 · Cited by 1,026
GeneCards: integrating information about genes, proteins and diseases
Rebhan, M. (1997) · Trends in Genetics · doi:10.1016/s0168-9525(97)01103-7 · Cited by 773
Rebhan, M., Chalifa-Caspi, V, Prilusky, J., & Lancet, D. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.8.656 · Cited by 500
Self-citationThe Mouse Genome Database (MGD): mouse biology and model systems
Bult, C. J., Eppig, J. T., Kadin, J. A., Richardson, J. E., Blake, J. A., & the Mouse Genome Database Group (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm961 · Cited by 414
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE
Safran, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg050 · Cited by 229
Self-citationGeneCards™ 2002: towards a complete, object-oriented, human gene compendium
Safran, M., Solomon, I., Shmueli, O., Lapidot, M., Shen-Orr, S., Adato, A., Ben-Dor, U., Esterman, N., Rosen, N., Peter, I., et al. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.11.1542 · Cited by 225
Self-citationGeneNote: whole genome expression profiles in normal human tissues
Shmueli, O., Horn-Saban, S., Chalifa-Caspi, V., Shmoish, M., Ophir, R., Benjamin-Rodrig, H., Safran, M., Domany, E., & Lancet, D. (2003) · Comptes Rendus. Biologies · doi:10.1016/j.crvi.2003.09.012 · Cited by 171
Self-citationNovel definition files for human GeneChips based on GeneAnnot
Ferrari, F., Bortoluzzi, S., Coppe, A., Sirota, A., Safran, M., Shmoish, M., Ferrari, S., Lancet, D., Danieli, G. A., & Bicciato, S. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-446 · Cited by 108
Self-citationGeneDecks: Paralog Hunting and Gene-Set Distillation with GeneCards Annotation
Stelzer, G., Inger, A., Olender, T., Stein, T. I., Dalah, I., Harel, A., Safran, M., & Lancet, D. (2009) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2009.0069 · Cited by 80
Self-citationGIFtS: annotation landscape analysis with GeneCards
Harel, A., Inger, A., Stelzer, G., Strichman-Almashanu, L. Z., Dalah, I., Safran, M., & Lancet, D. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-348 · Cited by 63
Self-citationGeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes
Chalifa‐Caspi, V., Yanai, I., Ophir, R., et al. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth081 · Cited by 63
GeneLoc: exon-based integration of human genome maps
Rosen, N., Chalifa‐Caspi, V., Shmueli, O., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1030 · Cited by 41
Self-citationShklar, M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki122 · Cited by 19
Rebhan, M., & Prilusky, J. (1997) · Electrophoresis · doi:10.1002/elps.1150181511 · Cited by 12
Cited by
STRING v10: protein–protein interaction networks, integrated over the tree of life
Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1003 · Cited by 10,436
The Reactome pathway Knowledgebase
Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1351 · Cited by 5,605
The GeneCards suite: from gene data mining to disease genome sequence analyses
Stelzer, G., Rosen, N., Plaschkes, I., Zimmerman, S., Twik, M., Fishilevich, S., Stein, T. I., Nudel, R., Lieder, I., Mazor, Y., et al. (2016) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.5 · Cited by 5,550
Self-citationALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility
Zheng, G., Dahl, J. A., Niu, Y., Fedorcsak, P., Huang, C.-M., Li, C. J., Vågbø, C. B., Shi, Y., Wang, W.-L., Song, S.-H., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.10.015 · Cited by 3,550
“We sorted the differentially expressed transcripts with reference to a compiled data set of reported spermatogenesis/infertility-related genes (Ashburner et al., 2000; Consortium, 2012; He et al., 2007; Pang et al., 2006; Rockett et al., 2004; Rossi et al., 2004; Safran et al., 2010; Shaha et al., 2010).”
Spatially resolved, highly multiplexed RNA profiling in single cells
Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X. (2015) · Science · doi:10.1126/science.aaa6090 · Cited by 2,969
Metadata
- Authors
- 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.
- Venue
- Database
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-08-05
- Volume
- 2010
- Issue
- 0
- Pages
- baq020-baq020
- ISSN
- 1758-0463 (ISSN-L)
- OpenAlex
- W2146980885
- Cited by
- 2,088
- References
- 18
- FWCI
- 16.19
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
