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

Makoto Shimada, Ryuzou Matsumoto, Yosuke Hayakawa, Ryoko Sanbonmatsu, Craig Gough, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Tadashi Imanishi, Takashi Gojobori

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

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/.

Original languageEnglish
JournalNucleic Acids Research
Volume37
Issue numberSUPPL. 1
DOIs
Publication statusPublished - 09-01-2009

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Genetic Databases
Medical Genetics
Genetic Polymorphisms
DNA Copy Number Variations
Linkage Disequilibrium
Alternative Splicing
Transcriptome
Microsatellite Repeats
Single Nucleotide Polymorphism
Genome
Databases
Phenotype
Gene Expression
Amino Acids
Messenger RNA
Research
Proteins

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Shimada, M., Matsumoto, R., Hayakawa, Y., Sanbonmatsu, R., Gough, C., Yamaguchi-Kabata, Y., ... Gojobori, T. (2009). VarySysDB: A human genetic polymorphism database based on all H-InvDB transcripts. Nucleic Acids Research, 37(SUPPL. 1). https://doi.org/10.1093/nar/gkn798
Shimada, Makoto ; Matsumoto, Ryuzou ; Hayakawa, Yosuke ; Sanbonmatsu, Ryoko ; Gough, Craig ; Yamaguchi-Kabata, Yumi ; Yamasaki, Chisato ; Imanishi, Tadashi ; Gojobori, Takashi. / VarySysDB : A human genetic polymorphism database based on all H-InvDB transcripts. In: Nucleic Acids Research. 2009 ; Vol. 37, No. SUPPL. 1.
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Shimada, M, Matsumoto, R, Hayakawa, Y, Sanbonmatsu, R, Gough, C, Yamaguchi-Kabata, Y, Yamasaki, C, Imanishi, T & Gojobori, T 2009, 'VarySysDB: A human genetic polymorphism database based on all H-InvDB transcripts', Nucleic Acids Research, vol. 37, no. SUPPL. 1. https://doi.org/10.1093/nar/gkn798

VarySysDB : A human genetic polymorphism database based on all H-InvDB transcripts. / Shimada, Makoto; Matsumoto, Ryuzou; Hayakawa, Yosuke; Sanbonmatsu, Ryoko; Gough, Craig; Yamaguchi-Kabata, Yumi; Yamasaki, Chisato; Imanishi, Tadashi; Gojobori, Takashi.

In: Nucleic Acids Research, Vol. 37, No. SUPPL. 1, 09.01.2009.

Research output: Contribution to journalArticle

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Shimada M, Matsumoto R, Hayakawa Y, Sanbonmatsu R, Gough C, Yamaguchi-Kabata Y et al. VarySysDB: A human genetic polymorphism database based on all H-InvDB transcripts. Nucleic Acids Research. 2009 Jan 9;37(SUPPL. 1). https://doi.org/10.1093/nar/gkn798