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Nucleic Acids Research Advance Access originally published online on October 25, 2008
Nucleic Acids Research 2009 37(Database issue):D810-D815; doi:10.1093/nar/gkn798
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Nucleic Acids Research, 2009, Vol. 37, Database issue D810-D815
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts

Makoto K. Shimada1,2, Ryuzou Matsumoto3, Yosuke Hayakawa2,3, Ryoko Sanbonmatsu1,2, Craig Gough1,2, Yumi Yamaguchi-Kabata1, Chisato Yamasaki1,2, Tadashi Imanishi1,* and Takashi Gojobori1,4

1Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2Japan Biological Informatics Consortium (JBIC), 3Hitachi Software Engineering Co., Ltd., Tokyo and 4Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Shizuoka, Japan

*To whom correspondence should be addressed. Tel: +81 3 3599 8800; Fax: +81 3 3599 8801; Email: t.imanishi{at}aist.go.jp

Correspondence may also be addressed to Takashi Gojobori. Tel: +81 55 981 6847; Fax: +81 55 981 6848; Email: tgojobor{at}genes.nig.ac.jp

Received August 14, 2008. Revised October 8, 2008. Accepted October 10, 2008.

Creation of a vast variety of proteins is accomplished by genetic variation and a variety of alternative splicing transcripts. Currently, however, the abundant available data on genetic variation and the transcriptome are stored independently and in a dispersed fashion. In order to provide a research resource regarding the effects of human genetic polymorphism on various transcripts, we developed VarySysDB, a genetic polymorphism database based on 187 156 extensively annotated matured mRNA transcripts from 36 073 loci provided by H-InvDB. VarySysDB offers information encompassing published human genetic polymorphisms for each of these transcripts separately. This allows comparisons of effects derived from a polymorphism on different transcripts. The published information we analyzed includes single nucleotide polymorphisms and deletion–insertion polymorphisms from dbSNP, copy number variations from Database of Genomic Variants, short tandem repeats and single amino acid repeats from H-InvDB and linkage disequilibrium regions from D-HaploDB. The information can be searched and retrieved by features, functions and effects of polymorphisms, as well as by keywords. VarySysDB combines two kinds of viewers, GBrowse and Sequence View, to facilitate understanding of the positional relationship among polymorphisms, genome, transcripts, loci and functional domains. We expect that VarySysDB will yield useful information on polymorphisms affecting gene expression and phenotypes. VarySysDB is available at http://h-invitational.jp/varygene/.

Present address: Makoto K. Shimada, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 470-1192, Japan


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