Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Grimmond, Sean M., Miranda, Kevin C., Yuan, Zheng, Davis, Melissa J., Hume, David A., Yagi, Ken, ...
We have developed a computational strategy to identify the set of soluble proteins secreted into the extracellular environment of a cell. Within the protein sequences predominantly derived from the...
Systematic Prediction of Orthologous Units of Genes (2002)
Hidemasa Bono, Susumu Goto, Wataru Fujibuchi, Hiroyuki Ogata, Minoru Kanehisa
In order to fully make use of the vast amount of information in the complete genome sequences, we are developing a genome-scale system for predicting gene functions and cellular functions. The system...
Practical Organization and Functional Annotation of RIKEN cDNA Microarray (2001)
Hidemasa Bono, Takeya Kasukawa, Rika Miki, Koji Kadota, Yasushi Okazaki, Yoshihide Hayashizaki
Introduction DNA microarray technology revolutionized gene expressionanalyss in molecularbiology to observe patterns of them in the genomic scale. As is often the case withnewly developed technology...
FANTOM+: The Interface for Functional Annotation of Mouse cDNA (2001)
Hidemasa Bono, Takeya Kasukawa, Toshihisa Okido, Katsunaga Sakai, Masaaki Furuno, Shotaro Kohtsuki, ...
Introduction RIKEN has been working on the mouse full-length cDNA encyclopedia since 1995. We have been focusing on the collection and sequencing of more than one million mouse cDNAs, hase I of the...
Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG (1999)
Mitsuteru Nakao, Hidemasa Bono, Shuichi Kawashima, Tomomi Kamiya, Kazushige Sato, Minoru Kanehisa
The massively parallel hybridization technologies by DNA chips and microarrays make it possible to monitor expression patterns of the whole set of genes in a genome under various conditions. The vast...
Sakai, Hiroe, Aoyama, Takashi, Bono, Hidemasa, Oka, Atsuhiro
An expression sequence tag database of higher plants was screened by in silico profile analysis for response regulators of the two-component regulatory system. Two closely related genes (ARR1 and...
Systematic Prediction of Orthologous Units of Genes in the Complete Genomes (1998)
Hidemasa Bono, Susumu Goto, Wataru Fujibuchi, Hiroyuki Ogata, Minoru Kanehisa
In order to fully make use of the vast amount of information in the complete genome sequences, we are developing a genome-scale system for predicting gene functions and cellular functions. The system...
Kotaro Shiraishi, Hiroko Ishida, Sanae Asanuma, Hidemasa Bono, Hiroyuki Ogata, Wataru Fujibuchi, ...
This paper focuses on how the GENES database is constructed and how gene annotations are made to maintain consistent information among species
Constructing and Annotating GENES Database in KEGG (1998)
Kotaro Shiraishi, Hiroko Ishida, Sanae Asanuma, Hidemasa Bono, Hiroyuki Ogata, Wataru Fujibuchi, ...
This paper focuses on how the GENES database is constructed and how gene annotations are made to maintain consistent information among species
Miki, Rika, Kadota, Koji, Bono, Hidemasa, Mizuno, Yosuke, Tomaru, Yasuhiro, Carninci, Piero, ...
We have systematically characterized gene expression patterns in 49 adult and embryonic mouse tissues by using cDNA microarrays with 18,816 mouse cDNAs. Cluster analysis defined sets of genes that...
READ: RIKEN Expression Array Database
Bono, Hidemasa, Kasukawa, Takeya, Hayashizaki, Yoshihide, Okazaki, Yasushi
READ, the RIKEN Expression Array Database, is a database of expression profile data from the RIKEN mouse cDNA microarray. It stores the microarray experimental data and information, and provides Web...
FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones
Bono, Hidemasa, Kasukawa, Takeya, Furuno, Masaaki, Hayashizaki, Yoshihide, Okazaki, Yasushi
FANTOM DB, the database of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to store sequence information of RIKEN full-length enriched mouse cDNA clones, graphical views of sequence...
Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data
Kochiwa, Hiromi, Suzuki, Ryosuke, Washio, Takanori, Saito, Rintaro, Bono, Hidemasa, ...
Although many studies on alternative splicing of specific genes have been reported in the literature, the general mechanism that regulates alternative splicing has not been clearly understood. In...
Protein–Protein Interaction Panel Using Mouse Full-Length cDNAs
Suzuki, Harukazu, Fukunishi, Yoshifumi, Kagawa, Ikuko, Saito, Rintaro, Oda, Hiroshi, Endo, Toshinori, ...
We have developed a novel assay system for systematic analysis of protein–protein interactions (PPIs) that is characteristic of a PCR-mediated rapid sample preparation and a high-throughput assay...
Gene discovery in genetically labeled single dopaminergic neurons of the retina
Gustincich, Stefano, Contini, Massimo, Gariboldi, Manuela, Puopolo, Michelino, Kadota, Koji, Bono, Hidemasa, ...
In the retina, dopamine plays a central role in neural adaptation to light. Progress in the study of dopaminergic amacrine (DA) cells has been limited because they are very few (450 in each mouse...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays
Bono, Hidemasa, Yagi, Ken, Kasukawa, Takeya, Nikaido, Itoshi, Tominaga, Naoko, Miki, Rika, ...
The number of known mRNA transcripts in the mouse has been greatly expanded by the RIKEN Mouse Gene Encyclopedia project. Validation of their reproducible expression in a tissue is an important...
Comprehensive Analysis of the Mouse Metabolome Based on the Transcriptome
Bono, Hidemasa, Nikaido, Itoshi, Kasukawa, Takeya, Hayashizaki, Yoshihide, Okazaki, Yasushi
The complete set of cDNAs encoding the enzymes of known metabolic pathways has not previously been available for any mammal. Here, transcripts encoding the metabolic pathways of the mouse (mouse...
Grimmond, Sean M., Miranda, Kevin C., Yuan, Zheng, Davis, Melissa J., Hume, David A., Yagi, Ken, ...
We have developed a computational strategy to identify the set of soluble proteins secreted into the extracellular environment of a cell. Within the protein sequences predominantly derived from the...
Wells, Christine A., Ravasi, Timothy, Sultana, Razvan, Yagi, Ken, Carninci, Piero, Bono, Hidemasa, ...
The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the...
Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System
Gustincich, Stefano, Batalov, Serge, Beisel, Kirk W., Bono, Hidemasa, Carninci, Piero, Fletcher, Colin F., ...
We analyzed the mouse Representative Transcript and Protein Set for molecules involved in brain function.We found full-length cDNAs of many known brain genes and discovered new members of known brain...
Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling
Nikaido, Itoshi, Saito, Chika, Mizuno, Yosuke, Meguro, Makiko, Bono, Hidemasa, Kadomura, Moritoshi, ...
Candidate imprinted transcriptional units in the mouse genome were identified systematically from 27,663 FANTOM2 full-length mouse cDNA clones by expression profiling. Large-scale cDNA microarrays...
G Protein-Coupled Receptor Genes in the FANTOM2 Database
Kawasawa, Yuka, McKenzie, Louise M., Hill, David P., Bono, Hidemasa, Yanagisawa, Masashi
G protein-coupled receptors (GPCRs) comprise the largest family of receptor proteins in mammals and play important roles in many physiological and pathological processes. Gene expression of GPCRs is...
Schriml, Lynn M., Hill, David P., Blake, Judith A., Bono, Hidemasa, Wynshaw-Boris, Anthony, Pavan, William J., ...
The FANTOM2 cDNA sequence data set is an excellent model to demonstrate the power of large-scale cDNA sequencing, with the goal of providing a full-length transcript sequence for each mouse gene....
Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
Kasukawa, Takeya, Furuno, Masaaki, Nikaido, Itoshi, Bono, Hidemasa, Hume, David A., Bult, Carol, ...
Manual curation has long been held to be the “gold standard” for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed...
Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
Carninci, Piero, Waki, Kazunori, Shiraki, Toshiyuki, Konno, Hideaki, Shibata, Kazuhiro, Itoh, Masayoshi, ...
We report the construction of the mouse full-length cDNA encyclopedia,the most extensive view of a complex transcriptome,on the basis of preparing and sequencing 246 libraries. Before cloning,cDNAs...
Miki, Rika, Kadota, Koji, Bono, Hidemasa, Mizuno, Yosuke, Tomaru, Yasuhiro, Carninci, Piero, ...
We have systematically characterized gene expression patterns in 49 adult and embryonic mouse tissues by using cDNA microarrays with 18,816 mouse cDNAs. Cluster analysis defined sets of genes that...
READ: RIKEN Expression Array Database
Bono, Hidemasa, Kasukawa, Takeya, Hayashizaki, Yoshihide, Okazaki, Yasushi
READ, the RIKEN Expression Array Database, is a database of expression profile data from the RIKEN mouse cDNA microarray. It stores the microarray experimental data and information, and provides Web...
FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones
Bono, Hidemasa, Kasukawa, Takeya, Furuno, Masaaki, Hayashizaki, Yoshihide, Okazaki, Yasushi
FANTOM DB, the database of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to store sequence information of RIKEN full-length enriched mouse cDNA clones, graphical views of sequence...
Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data
Kochiwa, Hiromi, Suzuki, Ryosuke, Washio, Takanori, Saito, Rintaro, Bono, Hidemasa, ...
Although many studies on alternative splicing of specific genes have been reported in the literature, the general mechanism that regulates alternative splicing has not been clearly understood. In...
Protein–Protein Interaction Panel Using Mouse Full-Length cDNAs
Suzuki, Harukazu, Fukunishi, Yoshifumi, Kagawa, Ikuko, Saito, Rintaro, Oda, Hiroshi, Endo, Toshinori, ...
We have developed a novel assay system for systematic analysis of protein–protein interactions (PPIs) that is characteristic of a PCR-mediated rapid sample preparation and a high-throughput assay...
Gene discovery in genetically labeled single dopaminergic neurons of the retina
Gustincich, Stefano, Contini, Massimo, Gariboldi, Manuela, Puopolo, Michelino, Kadota, Koji, Bono, Hidemasa, ...
In the retina, dopamine plays a central role in neural adaptation to light. Progress in the study of dopaminergic amacrine (DA) cells has been limited because they are very few (450 in each mouse...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays
Bono, Hidemasa, Yagi, Ken, Kasukawa, Takeya, Nikaido, Itoshi, Tominaga, Naoko, Miki, Rika, ...
The number of known mRNA transcripts in the mouse has been greatly expanded by the RIKEN Mouse Gene Encyclopedia project. Validation of their reproducible expression in a tissue is an important...
Comprehensive Analysis of the Mouse Metabolome Based on the Transcriptome
Bono, Hidemasa, Nikaido, Itoshi, Kasukawa, Takeya, Hayashizaki, Yoshihide, Okazaki, Yasushi
The complete set of cDNAs encoding the enzymes of known metabolic pathways has not previously been available for any mammal. Here, transcripts encoding the metabolic pathways of the mouse (mouse...
Grimmond, Sean M., Miranda, Kevin C., Yuan, Zheng, Davis, Melissa J., Hume, David A., Yagi, Ken, ...
We have developed a computational strategy to identify the set of soluble proteins secreted into the extracellular environment of a cell. Within the protein sequences predominantly derived from the...
Wells, Christine A., Ravasi, Timothy, Sultana, Razvan, Yagi, Ken, Carninci, Piero, Bono, Hidemasa, ...
The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the...
Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System
Gustincich, Stefano, Batalov, Serge, Beisel, Kirk W., Bono, Hidemasa, Carninci, Piero, Fletcher, Colin F., ...
We analyzed the mouse Representative Transcript and Protein Set for molecules involved in brain function.We found full-length cDNAs of many known brain genes and discovered new members of known brain...
Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling
Nikaido, Itoshi, Saito, Chika, Mizuno, Yosuke, Meguro, Makiko, Bono, Hidemasa, Kadomura, Moritoshi, ...
Candidate imprinted transcriptional units in the mouse genome were identified systematically from 27,663 FANTOM2 full-length mouse cDNA clones by expression profiling. Large-scale cDNA microarrays...
G Protein-Coupled Receptor Genes in the FANTOM2 Database
Kawasawa, Yuka, McKenzie, Louise M., Hill, David P., Bono, Hidemasa, Yanagisawa, Masashi
G protein-coupled receptors (GPCRs) comprise the largest family of receptor proteins in mammals and play important roles in many physiological and pathological processes. Gene expression of GPCRs is...
Schriml, Lynn M., Hill, David P., Blake, Judith A., Bono, Hidemasa, Wynshaw-Boris, Anthony, Pavan, William J., ...
The FANTOM2 cDNA sequence data set is an excellent model to demonstrate the power of large-scale cDNA sequencing, with the goal of providing a full-length transcript sequence for each mouse gene....
Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
Kasukawa, Takeya, Furuno, Masaaki, Nikaido, Itoshi, Bono, Hidemasa, Hume, David A., Bult, Carol, ...
Manual curation has long been held to be the “gold standard” for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed...
Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
Carninci, Piero, Waki, Kazunori, Shiraki, Toshiyuki, Konno, Hideaki, Shibata, Kazuhiro, Itoh, Masayoshi, ...
We report the construction of the mouse full-length cDNA encyclopedia,the most extensive view of a complex transcriptome,on the basis of preparing and sequencing 246 libraries. Before cloning,cDNAs...