Melissa J. Davis, Kelly A. Hanson, Francis Clark, J. Lynn Fink, Fasheng Zhang, Takeya Kasukawa, ...
Membrane organization describes the orientation of a protein with respect to the membrane and can be determined by the presence, or absence, and organization within the protein sequence of two...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Norihiro Maeda, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin Frith, Pär G. Engström, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine A, Chalk, Alistair M, Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
Abstract Background Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine, Chalk, Alistair Morgan, Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
BACKGROUND : Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine, Chalk, Alistair Morgan, Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
BACKGROUND : Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par G., ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par G., ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine, Chalk, Alistair Morgan, Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
BACKGROUND : Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par G., ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine A., Chalk, Alistair M., Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
Background: Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not...
Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs (2006)
Maeda, Norihiro, Kasukawa,Takeya, Frith, Martin, Aturaliya, Rajith N., Forrest, Alistair R. R., Ravasi,Timothy, ...
T he international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine A, Chalk, Alistair M, Forrest, Alistair Raymond Russell, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
Background Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine A, Chalk, Alistair M, Forrest, Alistair Raymond Russell, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
Background Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known...
Genome-wide analysis of mammalian promoter architecture and evolution (2006)
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, ...
Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We...
Alternate transcription of the Toll-like receptor signaling cascade (2006)
Wells, Christine A, Chalk, Alistair M, Forrest, Alistair Raymond Russell, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
Background Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
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...
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...
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...
Shiraki, Toshiyuki, Kondo, Shinji, Katayama, Shintaro, Waki, Kazunori, Kasukawa, Takeya, Kawaji, Hideya, ...
We introduce cap analysis gene expression (CAGE), which is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20 nucleotides from 5′ end mRNAs. CAGE allows...
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...
CDS Annotation in Full-Length cDNA Sequence
Furuno, Masaaki, Kasukawa, Takeya, Saito, Rintaro, Adachi, Jun, Suzuki, Harukazu, Baldarelli, Richard, ...
The identification of coding sequences (CDS) is an important step in the functional annotation of genes. CDS prediction for mammalian genes from genomic sequence is complicated by the vast abundance...
Connecting Sequence and Biology in the Laboratory Mouse
Baldarelli, Richard M., Hill, David P., Blake, Judith A., Adachi, Jun, Furuno, Masaaki, Bradt, Dirck, ...
The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These...
Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS
Nagashima, Takeshi, Silva, Diego G., Petrovsky, Nikolai, Socha, Luis A., Suzuki, Harukazu, Saito, Rintaro, ...
FACTS (Functional Association/Annotation of cDNA Clones from Text/Sequence Sources) is a semiautomated knowledge discovery and annotation system that integrates molecular function information derived...
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...
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis
Kawaji, Hideya, Kasukawa, Takeya, Fukuda, Shiro, Katayama, Shintaro, Kai, Chikatoshi, Kawai, Jun, ...
Cap-analysis gene expression (CAGE) Basic and Analysis Databases store an original resource produced by CAGE, which measures expression levels of transcription starting sites by sequencing large...
Alternate transcription of the Toll-like receptor signaling cascade
Wells, Christine A, Chalk, Alistair M, Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
A systematic analysis of the FANTOM3 mouse cDNA dataset provides transcriptional evidence of widespread alternate splicing in the Toll-like receptor signaling pathway.
Davis, Melissa J, Hanson, Kelly A, Clark, Francis, Fink, J. Lynn, Zhang, Fasheng, Kasukawa, Takeya, ...
Membrane organization describes the orientation of a protein with respect to the membrane and can be determined by the presence, or absence, and organization within the protein sequence of two...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engström, Pär G, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
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...
Shiraki, Toshiyuki, Kondo, Shinji, Katayama, Shintaro, Waki, Kazunori, Kasukawa, Takeya, Kawaji, Hideya, ...
We introduce cap analysis gene expression (CAGE), which is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20 nucleotides from 5′ end mRNAs. CAGE allows...
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...
CDS Annotation in Full-Length cDNA Sequence
Furuno, Masaaki, Kasukawa, Takeya, Saito, Rintaro, Adachi, Jun, Suzuki, Harukazu, Baldarelli, Richard, ...
The identification of coding sequences (CDS) is an important step in the functional annotation of genes. CDS prediction for mammalian genes from genomic sequence is complicated by the vast abundance...
Connecting Sequence and Biology in the Laboratory Mouse
Baldarelli, Richard M., Hill, David P., Blake, Judith A., Adachi, Jun, Furuno, Masaaki, Bradt, Dirck, ...
The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These...
Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS
Nagashima, Takeshi, Silva, Diego G., Petrovsky, Nikolai, Socha, Luis A., Suzuki, Harukazu, Saito, Rintaro, ...
FACTS (Functional Association/Annotation of cDNA Clones from Text/Sequence Sources) is a semiautomated knowledge discovery and annotation system that integrates molecular function information derived...
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...
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis
Kawaji, Hideya, Kasukawa, Takeya, Fukuda, Shiro, Katayama, Shintaro, Kai, Chikatoshi, Kawai, Jun, ...
Cap-analysis gene expression (CAGE) Basic and Analysis Databases store an original resource produced by CAGE, which measures expression levels of transcription starting sites by sequencing large...
Alternate transcription of the Toll-like receptor signaling cascade
Wells, Christine A, Chalk, Alistair M, Forrest, Alistair, Taylor, Darrin, Waddell, Nic, Schroder, Kate, ...
A systematic analysis of the FANTOM3 mouse cDNA dataset provides transcriptional evidence of widespread alternate splicing in the Toll-like receptor signaling pathway.
Davis, Melissa J, Hanson, Kelly A, Clark, Francis, Fink, J. Lynn, Zhang, Fasheng, Kasukawa, Takeya, ...
Membrane organization describes the orientation of a protein with respect to the membrane and can be determined by the presence, or absence, and organization within the protein sequence of two...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engström, Pär G, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Matsumoto, Akira, Ukai-Tadenuma, Maki, Yamada, Rikuhiro G., Houl, Jerry, Uno, Kenichiro D., Kasukawa, Takeya, ...
The Drosophila circadian clock consists of integrated autoregulatory feedback loops, making the clock difficult to elucidate without comprehensively identifying the network components in vivo....