AIST ∣ Biomedicinal Information Research Center (BIRC)

Integrated Database and Systems Biology Team

Integrated Database and Systems Biology Team develops an integrated database of all human genes and transcripts, H-Invitational Database (H-InvDB), and study biological phenomena such as evolution and gene expression by computational analyses of information about molecular systems.

Also, we carry out the Integrated Database Project of Ministry of Economy, Trade, and Industry of Japan (METI) in collaboration with the Japan Biological Informatics Consortium (JBIC), in order to promote the use of databases in the field of life science.

Mission

Integrated Database

Integrated Database and Systems Biology Team develops an integrated database of all human genes and transcripts using our original technology for gene annotation.

Our main research topics are ‘Structure and function of human alternative splicings,’ ‘Integrative annotation of human proteome,’ ‘Evolution of human genes by genomic duplication,’ ‘Diversity of human genes and its effects on gene function,’ ‘Evolution of human gene families by comparative genomics,’ ‘Origins and evolution of tissue-specific genes,’ and ‘Data-mining methods for identifying disease-related genes'.

Research result

We have constructed and made publicly available an integrated database of human genes by compiling results of functional annotation, diversity studies and comparative genomics studies.

　2010 　2009 　2008 　2007 　2006 　2005 　2004

2010

A comprehensive survey of human polymorphisms on conserved splice dinucleotides and its evolutionary relationship with alternative splicing.
BMC Evolutionary Biology, 10, 122.
Shimada MK, Hayakawa Y, Takeda J, Gojobori T and Imanishi T

2009

Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases.
NUCLEIC ACIDS RESEARCH, 37 (Web Server Issue): gkp355.
Imanishi T, and Nakaoka H

VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts.
NUCLEIC ACIDS RESEARCH, 37 (Web Server Issue): D810- D815.
Shimada MK, Matsumoto R, Hayakawa Y, Sanbonmatsu R, Gough C, Yamaguchi-Kabata Y, Yamasaki C, Imanishi T, and Gojobori T

H-InvDB in 2009, extended database and data mining resources for human genes and transcripts.
NUCLEIC ACIDS RESEARCH, 38 (Database Issue): D626-D632.
Yamasaki C, Murakami K, Takeda J, Sato Y, Noda A, Sakate R, Habara T, Nakaoka H, Todokoro F, Matsuya A, Imanishi T and Gojobori T

H-DBAS: Human-transcriptome DataBase for Alternative Splicing, update 2010.
NUCLEIC ACIDS RESEARCH, 38 (Database Issue): D86-D90.
Takeda J, Suzuki Y, Sakate R, Sato Y, Gojobori T, Imanishi T and Sugano S

G-compass: a web-based comparative genome browser between human and other vertebrate species.
Bioinformatics, 25, 3321-3322.
Kawahara Y, Sakate R, Matsuya A, Murakami K, Sato Y, Zhang H, Gojobori T, Itoh T and Imanishi T

2008

Low conservation and species-specific evolution of alternative splicing in humans and mice analysed with comparative genomics using well-annotated full-length cDNAs.
NUCLEIC ACIDS RESEARCH, 36 (20): 6386-6395.
Takeda J, Suzuki Y, Sakate R, Sato Y, Seki M, Irie T, Takeuchi N, Ueda T, Nakao M, Sugano S, Gojobori T and Imanishi T

Two different classes of co-occurring motif-pairs found by a novel visualization method in human promoter regions.
BMC GENOMICS, 9: 112.
Murakami M, Imanishi T, Gojobori T and Nakai K

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
Nucleic Acids Research, 36 (Database Issue): D793-D799.
Genome Information Integration Project and H-Invitational 2*
*Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo M, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares M, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, and Gojobori T.

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.
Nucleic Acids Research, 36 (Database Issue): D787-D792.
Matsuya A, Sakate R, Kawahara Y, Koyanagi KO, Sato Y, Fujii Y, Endo T, Ota S, Ikeo K, Suzuki Y, Hanada K, Iwama H, Makalowski W, Saitou N, Hiraki AT, Jin L, Kaneko Y, Kanno M, Murakami K, Noda A, Saichi N, Sanbonmatsu R, Suzuki M, Takeda J, Tanaka M, Yamasaki C, Gojobori T, Imanishi T, and Itoh T

2007

Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome.
GENE, 399 (1): 1-10.
Sakate R, Sato　Y, Imanishi　T, Tanoue T, Hida　M, Hayasaka I, Kusuda　J, Gojobori T, Hashimoto K and Hirai M

A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group.
BMC EVOLUTIONARY BIOLOGY, 7 (9): 13.
Kawahara Y, and Imanishi T

Cancer-related mutations in BRCA1-BRCT cause long-range structural changes in protein-protein binding sites: A molecular dynamics study.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 66 (1): 69-86.
Gough C, Gojobori T, and Imanishi T

H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-invitational.
NUCLEIC ACIDS RESEARCH, 35 (Database issue): D104-D109
Takeda J, Suzuki Y, Nakao M, Kuroda T, Sugano S, Gojobori T, and Imanishi T

2006

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs.
NUCLEIC ACIDS RESEARCH, 34 (14): 3917-3928.
Takeda J, Suzuki Y, Nakao M, Barrero RA, Koyanagi K, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V, Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T, and Imanishi T

TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB.
NUCLEIC ACIDS RESEARCH, 34 (Web Server issue): W345-W349.
Yamasaki C, Kawashima H, Todokoro F, Imamizu Y, Ogawa M, Tanino M, Itoh T, Gojobori T, and Imanishi T

2005

Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational Database (H-InvDB).
GENE, 364: 99-107.
Yamasaki C, Koyanagi K, Fujii Y, Itoh T, Barrero R A, Tamura T, Yamaguchi Y, Tanino M, Takeda J, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, and Gojobori T

A web tool for comparative genomics: G-compass.
GENE, 364: 45-52.
Fujii Y, Itoh T, Sakate R, Koyanagi K, Matsuya A, Habara T, Yamaguchi K, Kaneko Y, Gojobori T, and Imanishi T

Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system.
GENE, 353 (2): 169-176.
Koyanagi K, Hagiwara M, Itoh T, Gojobori T, and Imanishi T

The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv Integrative Display of Human Gene Expression across Disparate Technologies and Platforms.
NUCLEIC ACIDS RESEARCH, 33: D567-D572.
Tanino M, Debily M A, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza S J, Imbeaud S, Graudens E, Eveno E, Hilton P, Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide W, and Ookubo K

2004

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones.
PLoS Biology, 2: 856-875.
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, and Sugano S

Notes on the maximum likelihood estimation of haplotype frequencies.
Annals of Human Genetics, 68: 257-264.
Mano S, Yasuda N, Katoh T, Tounai K, Inoko H, Imanishi T, Tamiya G, and Gojobori T

Linkage of amino acid variation and evolution of human immunodeficiency virus type1 gp120 envelope glycoprotein (subtype B) linked with usage of the second receptor.
J. Mol. Evol, 58: 333-340.
Yamaguchi-Kabata Y, Yamashita M, Ohkura S, Hayami M. and Miura T