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

Genome Information Integration Project and H-Invitational 2 Consortium

Research output: Contribution to journalArticle

55 Citations (Scopus)

Abstract

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.

Original languageEnglish
JournalNucleic Acids Research
Volume36
Issue numberSUPPL. 1
DOIs
Publication statusPublished - 01-01-2008

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Databases
Genes
Molecular Sequence Annotation
Proteins
Transcriptome
Untranslated RNA
Pseudogenes
Alternative Splicing
Human Genome
Multigene Family
Rare Diseases
Metabolic Networks and Pathways
Microsatellite Repeats
Single Nucleotide Polymorphism
Cluster Analysis
Complementary DNA
Clone Cells
Messenger RNA

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Genome Information Integration Project and H-Invitational 2 Consortium. / The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. In: Nucleic Acids Research. 2008 ; Vol. 36, No. SUPPL. 1.
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abstract = "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.",
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The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. / Genome Information Integration Project and H-Invitational 2 Consortium.

In: Nucleic Acids Research, Vol. 36, No. SUPPL. 1, 01.01.2008.

Research output: Contribution to journalArticle

TY - JOUR

T1 - The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

AU - Genome Information Integration Project and H-Invitational 2 Consortium

AU - Yamasaki, Chisato

AU - Murakami, Katsuhiko

AU - Fujii, Yasuyuki

AU - Sato, Yoshiharu

AU - Harada, Erimi

AU - Takeda, Jun Ichi

AU - Taniya, Takayuki

AU - Sakate, Ryuichi

AU - Kikugawa, Shingo

AU - Shimada, Makoto

AU - Tanino, Motohiko

AU - Koyanagi, Kanako O.

AU - Barrero, Roberto A.

AU - Gough, Craig

AU - Chun, Hong Woo

AU - Habara, Takuya

AU - Hanaoka, Hideki

AU - Hayakawa, Yosuke

AU - Hilton, Phillip B.

AU - Kaneko, Yayoi

AU - Kanno, Masako

AU - Shimada, Makoto

AU - Kawamura, Toshiyuki

AU - Matsuya, Akihiro

AU - Nagata, Naoki

AU - Nishikata, Kensaku

AU - Noda, Akiko Ogura

AU - Nurimoto, Shin

AU - Saichi, Naomi

AU - Sakai, Hiroaki

AU - Sanbonmatsu, Ryoko

AU - Shiba, Rie

AU - Suzuki, Mami

AU - Takabayashi, Kazuhiko

AU - Takahashi, Aiko

AU - Tamura, Takuro

AU - Tanaka, Masayuki

AU - Tanaka, Susumu

AU - Todokoro, Fusano

AU - Yamaguchi, Kaori

AU - Yamamoto, Naoyuki

AU - Okido, Toshihisa

AU - Mashima, Jun

AU - Hashizume, Aki

AU - Jin, Lihua

AU - Lee, Kyung Bum

AU - Lin, Yi Chueh

AU - Nozaki, Asami

AU - Sakai, Katsunaga

AU - Tada, Masahito

PY - 2008/1/1

Y1 - 2008/1/1

N2 - 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.

AB - 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.

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JO - Nucleic Acids Research

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