66 research outputs found

    Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

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    The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

    Education level and incident functional disability in elderly Japanese: The Ohsaki Cohort 2006 study.

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    As the factors that link education level with incident functional disability in elderly Japanese have never been investigated, the present study investigated this issue in an elderly Japanese population. A 9-year prospective cohort study (2006-2015) was conducted among 8,680 Japanese individuals (ā‰„65 years), Ohsaki city, Japan. In a baseline survey, we collected data on education level and potential mediators. Data on incident functional disability were retrieved from the Long-term Care Insurance database. The Cox proportional hazards model was used to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs) for incident functional disability by education level (below upper-secondary education (reference), and upper secondary education and above). Mediating effects were estimated using accelerated failure time model and a logistic regression model. During 9-year follow-up period, 2,742 cases (31.6%) of incident functional disability were observed, and education level showed an inverse association with functional disability (P for trend <0.01). Participation in community activities had the largest mediating effect (34.7%) on the relationship between education level and incident functional disability. This effect remained among those aged 65-74 years (19.9%) but became negligible among those aged ā‰„75 years. Other potential mediators (such as smoking and drinking status) were also tested, but these showed only small mediating effects. The inverse association between education level and the incident risk of functional disability appears to be largely mediated by participation in community activities among elderly Japanese, especially those aged 65-74 years

    Effects of LLI, DAPT and combined application of both on cell proliferation.

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    <p>Proliferation ratios for each group at 24 h and 48 h after LLI for control (white bars), 60 min LLI (light grey bars), DAPT (grey bars) or the combination of LLI and DAPT (dark grey bars) are shown. Asterisks: one-way ANOVA, * p<0.05, ** p<0.01.</p
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