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

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/.

The rules of variation: Amino acid exchange according to the rotating circular genetic code

“…However, it advances the possibility for a stronger predictability of non-harmful variations, which is helpful for defining thousands of unclear changes under the current knowledge and databases. For example, in VarySysDB , the database recently developed by Shimada et al (2009), the next changes remain unclear, while by using the rules of variation reported here, we may conclude that in general, these variations were non-harmful: (1) Agrin (AGRN): Gtc / Atc bringing a Val/Ile change (Rule 1), (2) protein kinase C zeta (PRKCZ): ttC / ttG causing a Phe/Leu replacement (Rule 1), (3) Von Willebrand factor A domain-related protein isoform 1: gCg / gTg changing Ala/Val (Rule 3), (4) multiple epidermal growth factor-like domain 6 precursor (MEGF6): gCg / gTg causing Ala/Val change (Rule 3), and (5) stromal cell-derived factor 4 (SDF-4): Cag / Gag changing Gln/Glu (Rule 2).…”

Mapping complex disease traits with global gene expression

“…Transcription may also be modified by copy number variations (CNV), insertions and deletions, short tandem repeats and single amino acid repeats 23 . A systematic investigation of the effects of CNVs in individuals who are part of the International HapMap project showed that SNPs and CNVs captured 84% and 18% of the total detected genetic variation in gene expression, respectively, but the signals from the two types of variation had little overlap.…”

“…VarySysDB offers information encompassing published human genetic polymorphisms for each of these transcripts separately. In addition to SNP effects on transcription, this database includes deletion-insertion polymorphisms from dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/), copy number variations from Database of Genomic Variants (http://projects.tcag.ca/variation/), short tandem repeats and single amino acid repeats from H-InvDB (http://www.h-invitational.jp/) and linkage disequilibrium regions from D-HaploDB (http://orca.gen.kyushu-u.ac.jp/) 23 .…”

NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels

“…Other tools with a similar scope that were recently developed as, for example, SNPnexus [14] or VarySysDB [15] harness a variety of external data sources to characterize polymorphisms, but are based on static datasets restricted to human and offer only limited batch processing capabilities.…”