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

Genome Information Integration Project and H-Invitational 2 Consortium

doi:10.1093/nar/gkm999

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 journal › Article › peer-review

58 Scopus citations

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 language	English (US)
Pages (from-to)	D793-D799
Journal	NUCLEIC ACIDS RESEARCH
Volume	36
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkm999
State	Published - Jan 2008
Externally published	Yes

Bibliographical note

Funding Information:
We acknowledge all the members of the H-Invitational 2 consortium and Genome Information Integration Project (GIIP), especially the staffs of JBIRC for construction of H-InvDB, Ryo Aono, Tomohiro Endo, Yukie Makita, Hiromi Kubooka, Yuji Shinso, Harutoshi Maekawa, Yasuhiro Fukunaga, Hajime Nakaoka, Yoshito Ueki, Yoshihide Mimiura, Ryuzou Matsumoto, Seigo Hosoda, Yo Takahashi, Taichirou Sugisaki, Hiroki Hokari, Hiroaki Kawashima, Yasuhiro Imamizu, Makoto Ogawa for their technical assistance. This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program. Funding to pay the Open Access publication charges for this article was provided by JBIC.

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkm999

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@article{6f8bdddae6b3481fadc1a2561642388c,

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

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.",

author = "{Genome Information Integration Project and H-Invitational 2 Consortium} and Chisato Yamasaki and Katsuhiko Murakami and Yasuyuki Fujii and Yoshiharu Sato and Erimi Harada and Takeda, {Jun Ichi} and Takayuki Taniya and Ryuichi Sakate and Shingo Kikugawa and Makoto Shimada and Motohiko Tanino and Koyanagi, {Kanako O.} and Barrero, {Roberto A.} and Craig Gough and Chun, {Hong Woo} and Takuya Habara and Hideki Hanaoka and Yosuke Hayakawa and Hilton, {Phillip B.} and Yayoi Kaneko and Masako Kanno and Yoshihiro Kawahara and Toshiyuki Kawamura and Akihiro Matsuya and Naoki Nagata and Kensaku Nishikata and Noda, {Akiko Ogura} and Shin Nurimoto and Naomi Saichi and Hiroaki Sakai and Ryoko Sanbonmatsu and Rie Shiba and Mami Suzuki and Kazuhiko Takabayashi and Aiko Takahashi and Takuro Tamura and Masayuki Tanaka and Susumu Tanaka and Fusano Todokoro and Kaori Yamaguchi and Naoyuki Yamamoto and Toshihisa Okido and Jun Mashima and Aki Hashizume and Lihua Jin and Lee, {Kyung Bum} and Lin, {Yi Chueh} and Asami Nozaki and Hajime Ohyanagi and Takashi Gojobori",

note = "Funding Information: We acknowledge all the members of the H-Invitational 2 consortium and Genome Information Integration Project (GIIP), especially the staffs of JBIRC for construction of H-InvDB, Ryo Aono, Tomohiro Endo, Yukie Makita, Hiromi Kubooka, Yuji Shinso, Harutoshi Maekawa, Yasuhiro Fukunaga, Hajime Nakaoka, Yoshito Ueki, Yoshihide Mimiura, Ryuzou Matsumoto, Seigo Hosoda, Yo Takahashi, Taichirou Sugisaki, Hiroki Hokari, Hiroaki Kawashima, Yasuhiro Imamizu, Makoto Ogawa for their technical assistance. This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program. Funding to pay the Open Access publication charges for this article was provided by JBIC.",

year = "2008",

month = jan,

doi = "10.1093/nar/gkm999",

language = "English (US)",

volume = "36",

pages = "D793--D799",

journal = "NUCLEIC ACIDS RESEARCH",

issn = "0305-1048",

publisher = "OXFORD UNIV PRESS",

number = "SUPPL. 1",

}

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 - Kawahara, Yoshihiro

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 - Ohyanagi, Hajime

AU - Gojobori, Takashi

N1 - Funding Information: We acknowledge all the members of the H-Invitational 2 consortium and Genome Information Integration Project (GIIP), especially the staffs of JBIRC for construction of H-InvDB, Ryo Aono, Tomohiro Endo, Yukie Makita, Hiromi Kubooka, Yuji Shinso, Harutoshi Maekawa, Yasuhiro Fukunaga, Hajime Nakaoka, Yoshito Ueki, Yoshihide Mimiura, Ryuzou Matsumoto, Seigo Hosoda, Yo Takahashi, Taichirou Sugisaki, Hiroki Hokari, Hiroaki Kawashima, Yasuhiro Imamizu, Makoto Ogawa for their technical assistance. This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program. Funding to pay the Open Access publication charges for this article was provided by JBIC.

PY - 2008/1

Y1 - 2008/1

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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U2 - 10.1093/nar/gkm999

DO - 10.1093/nar/gkm999

M3 - Article

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AN - SCOPUS:38549163285

SN - 0305-1048

VL - 36

SP - D793-D799

JO - NUCLEIC ACIDS RESEARCH

JF - NUCLEIC ACIDS RESEARCH

IS - SUPPL. 1

ER -

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

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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