AAgAtlas 1.0

A human autoantigen database

Dan Wang, Liuhui Yang, Ping Zhang, Joshua LaBaer, Henning Hermjakob, Dong Li, Xiaobo Yu

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Autoantibodies refer to antibodies that target selfantigens, which can play pivotal roles in maintaining homeostasis, distinguishing normal from tumor tissue and trigger autoimmune diseases. In the last three decades, tremendous efforts have been devoted to elucidate the generation, evolution and functions of autoantibodies, as well as their target autoantigens. However, reports of these countless previously identified autoantigens are randomly dispersed in the literature. Here, we constructed an AAgAtlas database 1.0 using text-mining and manual curation. We extracted 45 830 autoantigen-related abstracts and 94 313 sentences from PubMed using the keywords of either 'autoantigen' or 'autoantibody' or their lexical variants, which were further refined to 25 520 abstracts, 43 253 sentences and 3984 candidates by our bio-entity recognizer based on the Protein Ontology. Finally, we identified 1126 genes as human autoantigens and 1071 related human diseases, with whichwe constructed a human autoantigen database (AAgAtlas database 1.0). The database provides a user-friendly interface to conveniently browse, retrieve and download human autoantigens as well as their associated diseases. The database is freely accessible at http://biokb.ncpsb.org/aagatlas/. We believe this database will be a valuable resource to track and understand human autoantigens as well as to investigate their functions in basic and translational research.

Original languageEnglish (US)
Pages (from-to)D769-D776
JournalNucleic Acids Research
Volume45
Issue numberD1
DOIs
StatePublished - Jan 1 2017

Fingerprint

Autoantigens
Databases
Autoantibodies
Translational Medical Research
Data Mining
PubMed
Autoimmune Diseases
Homeostasis
Antibodies
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Wang, D., Yang, L., Zhang, P., LaBaer, J., Hermjakob, H., Li, D., & Yu, X. (2017). AAgAtlas 1.0: A human autoantigen database. Nucleic Acids Research, 45(D1), D769-D776. https://doi.org/10.1093/nar/gkw946

AAgAtlas 1.0 : A human autoantigen database. / Wang, Dan; Yang, Liuhui; Zhang, Ping; LaBaer, Joshua; Hermjakob, Henning; Li, Dong; Yu, Xiaobo.

In: Nucleic Acids Research, Vol. 45, No. D1, 01.01.2017, p. D769-D776.

Research output: Contribution to journalArticle

Wang, D, Yang, L, Zhang, P, LaBaer, J, Hermjakob, H, Li, D & Yu, X 2017, 'AAgAtlas 1.0: A human autoantigen database', Nucleic Acids Research, vol. 45, no. D1, pp. D769-D776. https://doi.org/10.1093/nar/gkw946
Wang D, Yang L, Zhang P, LaBaer J, Hermjakob H, Li D et al. AAgAtlas 1.0: A human autoantigen database. Nucleic Acids Research. 2017 Jan 1;45(D1):D769-D776. https://doi.org/10.1093/nar/gkw946
Wang, Dan ; Yang, Liuhui ; Zhang, Ping ; LaBaer, Joshua ; Hermjakob, Henning ; Li, Dong ; Yu, Xiaobo. / AAgAtlas 1.0 : A human autoantigen database. In: Nucleic Acids Research. 2017 ; Vol. 45, No. D1. pp. D769-D776.
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