Osada, Naoki, Hashimoto, Katsuyuki, Kameoka, Yosuke, Hirata, Makoto, Tanuma, Reiko, Uno, Yasuhiro, ...
Abstract Background Cynomolgus macaques ( Macaca fascicularis ) are widely used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as rhesus...
Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates (2007)
Hurng-Yi Wang, Huan-Chieh Chien, Naoki Osada, Katsuyuki Hashimoto, Sumio Sugano, Takashi Gojobori, ...
Brain-expressed genes are known to evolve slowly in mammals. Nevertheless, since brains of higher primates have evolved rapidly, one might expect acceleration in DNA sequence evolution in their...
Saito, Ayumu, Nagasaki, Masao, Oyama, Masaaki, Kozuka-Hata, Hiroko, Semba, Kentaro, Sugano, Sumio, ...
Abstract Background Comprehensive description of the behavior of cellular components in a quantitative manner is essential for systematic understanding of biological events. Recent LC-MS/MS (tandem...
Genome Informatics 14: 456--457 (2003) The Translated Region Inspector for cDNA Sequences (2004)
Kouichi Kimura, Tetsuo Nisikawa, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai
Introduction The human genome sequencing project is now being to complete the final stage of building the finished sequences. However, transcriptome sequencing will remain far from completion for...
Genome Informatics 14: 404--405 (2003) Genome Wide Analysis Reveals Strong Correlation (2004)
Riu Yamashita, Toshihisa Takagi, Sumio Sugano, Kenta Nakai
Introduction Vertebrate genomes contain GC-rich or poor compartments, called isochores, It has been reported that heavy isochores (GC-rich) contain housekeeping genes while light ischores (GC-rich)...
Tetsuo Nishikawa, Kouichi Kimura, Tomohiro Yasuda, Jun-ichi Yamamoto, Ai Wakamatsu, Shizuko Ishii, ...
Introduction Whole human genome sequence determination was completed this year. To obtain accurate gene structures and promoter information, full-length cDNA sequence information as well as the...
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...
Stochastic Indicator of Regions and Application to (2003)
Kouichi Kimura, Tetsuo Nishikawa, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai
Local prediction of regions in a sequence is considered, where the sequence is assumed to be generated by a doubly stochastic Markov model and its transition probabilities are assumed to remain...
Osada, Naoki, Hida, Munetomo, Kusuda, Jun, Tanuma, Reiko, Hirata, Makoto, Suto, Yumiko, ...
Abstract Background In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and...
Osada, Naoki, Hida, Munetomo, Kusuda, Jun, Tanuma, Reiko, Hirata, Makoto, Hirai, Momoki, ...
Abstract Background The complete assignment of the protein-coding regions of the human genome is a major challenge for genome biology today. We have already isolated many hitherto unknown full-length...
Watanabe, Junichi, Sasaki, Masahide, Suzuki, Yutaka, Sugano, Sumio
FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum (http://133.11.149.55/). Because of its medical importance, this organism is...
HUNT: launch of a full-length cDNA database from the Helix Research Institute
Yudate, Henrik T., Suwa, Makiko, Irie, Ryotaro, Matsui, Hiroshi, Nishikawa, Tetsuo, Nakamura, Yoshitaka, ...
The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project...
Omori, Yoshihiro, Imai, Jun-ichi, Watanabe, Manabu, Komatsu, Takami, Suzuki, Yutaka, Kataoka, Kohsuke, ...
The expression of liver-specific genes is regulated by unequivocally allocated transcription factors via proper responsible elements within their promoters. We identified a novel transcription...
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
Suzuki, Yutaka, Yamashita, Riu, Nakai, Kenta, Sugano, Sumio
Although the information of cDNAs is indispensable for analyzing gene function, most of the cDNA sequences stored in current databases are imperfect in the sense that they lack the precise...
Internal ribosome entry site-mediated translation of Smad5 in vivo: requirement for a nuclear event
Shiroki, Kazuko, Ohsawa, Chieko, Sugi, Natuki, Wakiyama, Motoaki, Miura, Kin-ichiro, Watanabe, Manabu, ...
Smad5 is thought to relay signals of the bone morphogenetic protein pathway. The 5′ untranslated region (5′UTR) of human Smad5 mRNA is long, has the potential to form secondary structures and...
Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence
Osada, Naoki, Hida, Munetomo, Kusuda, Jun, Tanuma, Reiko, Hirata, Makoto, Suto, Yumiko, ...
Jin, Yui, Suzuki, Hitoshi, Maegawa, Shingo, Endo, Hitoshi, Sugano, Sumio, Hashimoto, Katsuyuki, ...
Alternative splicing is one of the central mechanisms that regulate eukaryotic gene expression. Here we report a tissue-specific RNA-binding protein, Fox-1, which regulates alternative splicing in...
Osada, Naoki, Hida, Munetomo, Kusuda, Jun, Tanuma, Reiko, Hirata, Makoto, Hirai, Momoki, ...
Twenty-nine novel human genes were predicted with putative coding regions sharing an open reading frame with the cynomolgus monkey, and the expression of 21 pairs of genes was confirmed by reverse...
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
Suzuki, Yutaka, Yamashita, Riu, Sugano, Sumio, Nakai, Kenta
DBTSS (http://dbtss.hgc.jp) was originally constructed based on a collection of experimentally determined TSSs of human genes. Since its first release in 2002, it has been updated several times....
Watanabe, Junichi, Suzuki, Yutaka, Sasaki, Masahide, Sugano, Sumio
Full-malaria (http://fullmal.ims.u-tokyo.ac.jp), a database for full-length cDNAs from the human malaria parasite, Plasmodium falciparum has been updated in at least three points. (i) We added 8934...
CART Classification of Human 5′ UTR Sequences
Davuluri, Ramana V., Suzuki, Yutaka, Sugano, Sumio, Zhang, Michael Q.
A nonredundant database of 2312 full-length human 5′-untranslated regions (UTRs) was carefully prepared using state-of-the-art experimental and computational technologies. A comprehensive...
Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes
Suzuki, Yutaka, Tsunoda, Tatsuhiko, Sese, Jun, Taira, Hirotoshi, Mizushima-Sugano, Junko, Hata, Hiroko, ...
To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from...
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...
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
Clark, Melody S., Edwards, Yvonne J.K., Peterson, Dan, Clifton, Sandra W., Thompson, Amanda J., Sasaki, Masahide, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
Analysis of 5′-End Sequences of Chimpanzee cDNAs
Sakate, Ryuichi, Osada, Naoki, Hida, Munetomo, Sugano, Sumio, Hayasaka, Ikuo, Shimohira, Naoko, ...
We constructed full-length enriched cDNA libraries from chimpanzee brain, skin, and liver tissues by the oligo-capping method to establish a database of sequences of chimpanzee genes. Randomly...
GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene
Huang, Duen-Yi, Kuo, Yuan-Yeh, Lai, Jiann-Shiun, Suzuki, Yutaka, Sugano, Sumio, Chang, Zee-Fen
Expression of Gfi (growth factor-independence)-1B, a Gfi-1-related transcriptional repressor, is restricted to erythroid lineage cells and is essential for erythropoiesis. We have determined the...
Suzuki, Yutaka, Yamashita, Riu, Shirota, Matsuyuki, Sakakibara, Yuta, Chiba, Joe, Mizushima-Sugano, Junko, ...
Comparative sequence analysis was carried out for the regions adjacent to experimentally validated transcriptional start sites (TSSs), using 3324 pairs of human and mouse genes. We aligned the...
Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs
Oyama, Masaaki, Itagaki, Chiharu, Hata, Hiroko, Suzuki, Yutaka, Izumi, Tomonori, Natsume, Tohru, ...
To find novel short coding sequences from accumulated full-length cDNA sequences, proteomic analysis of small proteins expressed in human leukemia K562 cells was performed using high-resolution...
5′SAGE: 5′-end Serial Analysis of Gene Expression database
Kasai, Yasuhiro, Hashimoto, Shin-ichi, Yamada, Tomoyuki, Sese, Jun, Sugano, Sumio, Matsushima, Kouji, ...
To comprehensively identify transcription start sites and the frequencies of individual mRNAs in human cell libraries, a method of 5′ end Serial Analysis of Gene Expression (SAGE) was developed...
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
Suzuki, Yutaka, Taira, Hirotoshi, Tsunoda, Tatsuhiko, Mizushima-Sugano, Junko, Sese, Jun, Hata, Hiroko, ...
Determination of the mRNA start site is the first step in identifying the promoter region, which is of key importance for transcriptional regulation of gene expression. The ‘oligo-capping’ method...
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006
Yamashita, Riu, Suzuki, Yutaka, Wakaguri, Hiroyuki, Tsuritani, Katsuki, Nakai, Kenta, Sugano, Sumio
DBTSS was first constructed in 2002 based on precise, experimentally determined 5′ end clones. Several major updates and additions have been made since the last report. First, the number of human...
Kimura, Kouichi, Wakamatsu, Ai, Suzuki, Yutaka, Ota, Toshio, Nishikawa, Tetsuo, Yamashita, Riu, ...
By analyzing 1,780,295 5′-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
Watanabe, Junichi, Sasaki, Masahide, Suzuki, Yutaka, Sugano, Sumio
FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum (http://133.11.149.55/). Because of its medical importance, this organism is...
HUNT: launch of a full-length cDNA database from the Helix Research Institute
Yudate, Henrik T., Suwa, Makiko, Irie, Ryotaro, Matsui, Hiroshi, Nishikawa, Tetsuo, Nakamura, Yoshitaka, ...
The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project...
Omori, Yoshihiro, Imai, Jun-ichi, Watanabe, Manabu, Komatsu, Takami, Suzuki, Yutaka, Kataoka, Kohsuke, ...
The expression of liver-specific genes is regulated by unequivocally allocated transcription factors via proper responsible elements within their promoters. We identified a novel transcription...
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
Suzuki, Yutaka, Yamashita, Riu, Nakai, Kenta, Sugano, Sumio
Although the information of cDNAs is indispensable for analyzing gene function, most of the cDNA sequences stored in current databases are imperfect in the sense that they lack the precise...
Internal ribosome entry site-mediated translation of Smad5 in vivo: requirement for a nuclear event
Shiroki, Kazuko, Ohsawa, Chieko, Sugi, Natuki, Wakiyama, Motoaki, Miura, Kin-ichiro, Watanabe, Manabu, ...
Smad5 is thought to relay signals of the bone morphogenetic protein pathway. The 5′ untranslated region (5′UTR) of human Smad5 mRNA is long, has the potential to form secondary structures and...
Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence
Osada, Naoki, Hida, Munetomo, Kusuda, Jun, Tanuma, Reiko, Hirata, Makoto, Suto, Yumiko, ...
Jin, Yui, Suzuki, Hitoshi, Maegawa, Shingo, Endo, Hitoshi, Sugano, Sumio, Hashimoto, Katsuyuki, ...
Alternative splicing is one of the central mechanisms that regulate eukaryotic gene expression. Here we report a tissue-specific RNA-binding protein, Fox-1, which regulates alternative splicing in...
Osada, Naoki, Hida, Munetomo, Kusuda, Jun, Tanuma, Reiko, Hirata, Makoto, Hirai, Momoki, ...
Twenty-nine novel human genes were predicted with putative coding regions sharing an open reading frame with the cynomolgus monkey, and the expression of 21 pairs of genes was confirmed by reverse...
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
Suzuki, Yutaka, Yamashita, Riu, Sugano, Sumio, Nakai, Kenta
DBTSS (http://dbtss.hgc.jp) was originally constructed based on a collection of experimentally determined TSSs of human genes. Since its first release in 2002, it has been updated several times....
Watanabe, Junichi, Suzuki, Yutaka, Sasaki, Masahide, Sugano, Sumio
Full-malaria (http://fullmal.ims.u-tokyo.ac.jp), a database for full-length cDNAs from the human malaria parasite, Plasmodium falciparum has been updated in at least three points. (i) We added 8934...
CART Classification of Human 5′ UTR Sequences
Davuluri, Ramana V., Suzuki, Yutaka, Sugano, Sumio, Zhang, Michael Q.
A nonredundant database of 2312 full-length human 5′-untranslated regions (UTRs) was carefully prepared using state-of-the-art experimental and computational technologies. A comprehensive...
Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes
Suzuki, Yutaka, Tsunoda, Tatsuhiko, Sese, Jun, Taira, Hirotoshi, Mizushima-Sugano, Junko, Hata, Hiroko, ...
To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from...
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...
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
Clark, Melody S., Edwards, Yvonne J.K., Peterson, Dan, Clifton, Sandra W., Thompson, Amanda J., Sasaki, Masahide, ...
The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis...
Analysis of 5′-End Sequences of Chimpanzee cDNAs
Sakate, Ryuichi, Osada, Naoki, Hida, Munetomo, Sugano, Sumio, Hayasaka, Ikuo, Shimohira, Naoko, ...
We constructed full-length enriched cDNA libraries from chimpanzee brain, skin, and liver tissues by the oligo-capping method to establish a database of sequences of chimpanzee genes. Randomly...
GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene
Huang, Duen-Yi, Kuo, Yuan-Yeh, Lai, Jiann-Shiun, Suzuki, Yutaka, Sugano, Sumio, Chang, Zee-Fen
Expression of Gfi (growth factor-independence)-1B, a Gfi-1-related transcriptional repressor, is restricted to erythroid lineage cells and is essential for erythropoiesis. We have determined the...
Suzuki, Yutaka, Yamashita, Riu, Shirota, Matsuyuki, Sakakibara, Yuta, Chiba, Joe, Mizushima-Sugano, Junko, ...
Comparative sequence analysis was carried out for the regions adjacent to experimentally validated transcriptional start sites (TSSs), using 3324 pairs of human and mouse genes. We aligned the...
Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs
Oyama, Masaaki, Itagaki, Chiharu, Hata, Hiroko, Suzuki, Yutaka, Izumi, Tomonori, Natsume, Tohru, ...
To find novel short coding sequences from accumulated full-length cDNA sequences, proteomic analysis of small proteins expressed in human leukemia K562 cells was performed using high-resolution...
5′SAGE: 5′-end Serial Analysis of Gene Expression database
Kasai, Yasuhiro, Hashimoto, Shin-ichi, Yamada, Tomoyuki, Sese, Jun, Sugano, Sumio, Matsushima, Kouji, ...
To comprehensively identify transcription start sites and the frequencies of individual mRNAs in human cell libraries, a method of 5′ end Serial Analysis of Gene Expression (SAGE) was developed...
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
Suzuki, Yutaka, Taira, Hirotoshi, Tsunoda, Tatsuhiko, Mizushima-Sugano, Junko, Sese, Jun, Hata, Hiroko, ...
Determination of the mRNA start site is the first step in identifying the promoter region, which is of key importance for transcriptional regulation of gene expression. The ‘oligo-capping’ method...
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006
Yamashita, Riu, Suzuki, Yutaka, Wakaguri, Hiroyuki, Tsuritani, Katsuki, Nakai, Kenta, Sugano, Sumio
DBTSS was first constructed in 2002 based on precise, experimentally determined 5′ end clones. Several major updates and additions have been made since the last report. First, the number of human...
Kimura, Kouichi, Wakamatsu, Ai, Suzuki, Yutaka, Ota, Toshio, Nishikawa, Tetsuo, Yamashita, Riu, ...
By analyzing 1,780,295 5′-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...