H-InvDB in 2009: Extended database and data mining resources for human genes and transcripts

Chisato Yamasaki; Katsuhiko Murakami; Jun ichi Takeda; Yoshiharu Sato; Akiko Noda; Ryuichi Sakate; Takuya Habara; Hajime Nakaoka; Fusano Todokoro; Akihiro Matsuya; Tadashi Imanishi; Takashi Gojobori

doi:10.1093/nar/gkp1020

H-InvDB in 2009: Extended database and data mining resources for human genes and transcripts

Chisato Yamasaki, Katsuhiko Murakami, Jun ichi Takeda, Yoshiharu Sato, Akiko Noda, Ryuichi Sakate, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, Akihiro Matsuya, Tadashi Imanishi, Takashi Gojobori^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

37 Scopus citations

Abstract

We report the extended database and data mining resources newly released in the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). H-InvDB is a comprehensive annotation resource of human genes and transcripts, and consists of two main views and six sub-databases. The latest release of H-InvDB (release 6.2) provides the annotation for 219 765 human transcripts in 43 159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs. 'Navigation search' is an extended search system that enables complicated searches by combining 16 different search options. HEAT is a data mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. H-InvDB now has web service APIs of SOAP and REST to allow the use of H-InvDB data in programs, providing the users extended data accessibility.

Original language	English (US)
Article number	gkp1020
Pages (from-to)	D626-D632
Journal	NUCLEIC ACIDS RESEARCH
Volume	38
Issue number	SUPPL.1
DOIs	https://doi.org/10.1093/nar/gkp1020
State	Published - Nov 23 2009
Externally published	Yes

ASJC Scopus subject areas

Genetics

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abstract = "We report the extended database and data mining resources newly released in the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). H-InvDB is a comprehensive annotation resource of human genes and transcripts, and consists of two main views and six sub-databases. The latest release of H-InvDB (release 6.2) provides the annotation for 219 765 human transcripts in 43 159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs. 'Navigation search' is an extended search system that enables complicated searches by combining 16 different search options. HEAT is a data mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. H-InvDB now has web service APIs of SOAP and REST to allow the use of H-InvDB data in programs, providing the users extended data accessibility.",

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AU - Sato, Yoshiharu

AU - Noda, Akiko

AU - Sakate, Ryuichi

AU - Habara, Takuya

AU - Nakaoka, Hajime

AU - Todokoro, Fusano

AU - Matsuya, Akihiro

AU - Imanishi, Tadashi

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H-InvDB in 2009: Extended database and data mining resources for human genes and transcripts

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