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- Imanishi, T., et al.
(författare)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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- Udalski, A., et al.
(författare)
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OGLE-2017-BLG-1434Lb : Eighth q < 1 x 10(-4) Mass-Ratio Microlens Planet Confirms Turnover in Planet Mass-Ratio Function
- 2018
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Ingår i: Acta Astronomica. - 0001-5237. ; 68:1, s. 1-42
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of a cold Super-Earth planet (m(p) = 4.4 +/- 0.5 M-circle plus) orbiting a low-mass (M = 0.23 +/- 0.03 M-circle dot) M dwarf at projected separation a(perpendicular to) l = 1.18 +/- 0.10 a.u., i.e., about 1.9 times the distance the snow line. The system is quite nearby for a microlensing planet, D-L = 0.86 +/- 0.09 kpc. Indeed, it was the large lens-source relative parallax pi(rel) = 1.0 mas (combined with the low mass M) that gave rise to the large, and thus well-measured, microlens parallax pi(E) proportional to (pi(rel)/M)(1)(/2) that enabled these precise measurements. OGLE-2017-BLG-1434Lb is the eighth microlensing planet with planet-host mass ratio q < 1 x 10(-4). We apply a new planet-detection sensitivity method, which is a variant of V/V-max, to seven of these eight planets to derive the mass-ratio function in this regime. We find dN/ d lnq proportional to q(P) , with p =1.05(-0.68)(+0.78), which confirms the turnover in the mass function found by Suzuki et al. relative to the power law of opposite sign n = -0.93 +/- 0.13 at higher mass ratios q greater than or similar to 2 x 10(-4). We combine our result with that of Suzuki et al. to obtain p = 0.73(-0.34)(+0.42.)
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- Antfolk, M., et al.
(författare)
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An integrated acousto- and dielectrophoresis device for tumor cell separation, concentration, and single-cell trapping
- 2016
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Ingår i: 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016. - 9780979806490 ; , s. 1657-1658
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Konferensbidrag (refereegranskat)abstract
- Many microfluidic devices have been developed to separate rare cells, e.g. circulating tumor cells. The collection and analysis of the separated rare cells pose a challenge as it may lead to loss of target cells since extremely small number of cells are usually suspended in a large volume after separation. Here, we present an integrated device that allows acoustophoretic target cell separation and concentration, followed by dielectrophoretic single-cell trapping. We show that the human prostate cancer cell line DU145 were efficiently separated from peripheral blood mononuclear cells (PBMCs), and 81.7% of DU145 were trapped, with a contamination of 1.7% PBMC.
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