The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

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概要

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• Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein–protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.

著者

• Morisaki Takayuki

  国立循環器病センター 心臓血管内科

• Sugano Sumio

  放射線医学総合研究所

• Sugano Sumio

  Helix Research Institute

• Hanada Hironori

  Research Institute National Cardiovascular Center

• Sugano Sumio

  Department Of Virology Institute Of Medical Science University Of Tokyo

• Morisaki T

  Department Of Bioscience National Cardiovascular Center Research Institute

• Suzuki Yoichi

  Department Of Medical Genetics Tohoku University School Of Medicine

• NISHIKAWA Ken

  National Institute of Genetics

• Sugano Sumio

  University Of Tokyo

• Miyazaki J

  Univ. Tsukuba Ibaraki Jpn

• Suzuki Yutaka

  University of Tokyo

• Nakai Kenta

  University of Tokyo

• Yamamoto Takako

  Department Of Health Science Shiga University Of Medical Science

• Yura K

  Department Of Biological Science Graduate School Of Science Nagoya University

• Yura Kei

  Quantum Bioinfo. Jaea

• Ohtsubo Masafumi

  Medical Photobiology Department Photon Medical Research Center Hamamatsu University School Of Medici

• Sakata Yoshiyuki

  Department Of Medical Genetics Tohoku University School Of Medicine

• Suzuki Y

  Department Of Medical Genetics Tohoku University School Of Medicine

• SUZUKI Yasuyo

  Department of Clinical Genetics, Medical Institute of Bioregulation, Kyushu University

• Mashima Jun

  Institute Of Biological Sciences University Of Tsukuba:(present Address)school Of Life Science Unive

• Go Mitiko

  Fac. Bio-sci. Nagahama Inst. Bio-sci. Tech.:ochanomizu Univ.

• HATTA Yosuke

  Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology

• SHIONYU Masafumi

  Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology

• Suwa Makiko

  Computational Biology Research Center (cbrc) National Institute Of Advanced Industrial Science And T

• Shionyu Masafumi

  Department Of Bioscience Faculty Of Bioscience Nagahama Institute Of Bio-science And Technology

• Mukai Yuri

  Department Of Electronics And Bioinformatics School Of Science And Technology Meiji University

• Fukuchi Satoshi

  Maebashi Institute of Technology

• Miura Toshie

  Department Of Ophthalmology Hokkaido University Graduate School Of Medicine

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