PREFACE:

Yoshihide Hayashizaki

Special FANTOM2 Issue
Genome Res. 2003 13: 1265. [Full Text]  

COMMENTARY:

Yasushi Okazaki and David A. Hume

A Guide to the Mammalian Genome
Genome Res. 2003 13: 1267-1272. [Full Text]  

ARTICLES:

Piero Carninci, Kazunori Waki, Toshiyuki Shiraki, Hideaki Konno, Kazuhiro Shibata, Masayoshi Itoh, Katsunori Aizawa, Takahiro Arakawa, Yoshiyuki Ishii, Daisuke Sasaki, Hidemasa Bono, Shinji Kondo, Yuichi Sugahara, Rintaro Saito, Naoki Osato, Shiro Fukuda, Kenjiro Sato, Akira Watahiki, Tomoko Hirozane-Kishikawa, Mari Nakamura, Yuko Shibata, Ayako Yasunishi, Noriko Kikuchi, Atsushi Yoshiki, Moriaki Kusakabe, Stefano Gustincich, Kirk Beisel, William Pavan, Vassilis Aidinis, Akira Nakagawara, William A. Held, Hiroo Iwata, Tomohiro Kono, Hiromitsu Nakauchi, Paul Lyons, Christine Wells, David A. Hume, Michela Fagiolini, Takao K. Hensch, Michelle Brinkmeier, Sally Camper, Junji Hirota, Peter Mombaerts, Masami Muramatsu, Yasushi Okazaki, Jun Kawai, and Yoshihide Hayashizaki

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
Genome Res. 2003 13: 1273-1289. [Abstract] [Full Text] [Supplemental Research Data]  

Mihaela Zavolan, Shinji Kondo, Christian Schönbach, Jun Adachi, David A. Hume, RIKEN GER Group, GSL Members, Yoshihide Hayashizaki, and Terry Gaasterland

Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome
Genome Res. 2003 13: 1290-1300. [Abstract] [Full Text] [Supplemental Research Data]  

Koji Numata, Akio Kanai, Rintaro Saito, Shinji Kondo, Jun Adachi, Laurens G. Wilming, David A. Hume, RIKEN GER Group, GSL Members, Yoshihide Hayashizaki, and Masaru Tomita

Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection
Genome Res. 2003 13: 1301-1306. [Abstract] [Full Text] [Supplemental Research Data]  

Vladimir Brusic, Rekha S. Pillai, Diego G. Silva, Nikolai Petrovsky, RIKEN GER Group, GSL Members, and Christian Schönbach

Cytokine-Related Genes Identified From the RIKEN Full-Length Mouse cDNA Data Set
Genome Res. 2003 13: 1307-1317. [Abstract] [Full Text] [Supplemental Research Data]  

LETTERS:

Hidemasa Bono, Ken Yagi, Takeya Kasukawa, Itoshi Nikaido, Naoko Tominaga, Rika Miki, Yosuke Mizuno, Yasuhiro Tomaru, Hitoshi Goto, Hiroyuki Nitanda, Daisuke Shimizu, Hirochika Makino, Tomoyuki Morita, Junshin Fujiyama, Takehito Sakai, Takashi Shimoji, David A. Hume, Yoshihide Hayashizaki, and Yasushi Okazaki

Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays
Genome Res. 2003 13: 1318-1323. [Abstract] [Full Text] [Supplemental Research Data]  

Hidenori Kiyosawa, Itaru Yamanaka, Naoki Osato, Shinji Kondo, and Yoshihide Hayashizaki

Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation
Genome Res. 2003 13: 1324-1334. [Abstract] [Full Text]  

Alexander Kanapin, Serge Batalov, Melissa J. Davis, Julian Gough, Sean Grimmond, Hideya Kawaji, Michele Magrane, Hideo Matsuda, Christian Schönbach, Rohan D. Teasdale, and Zheng Yuan

Mouse Proteome Analysis
Genome Res. 2003 13: 1335-1344. [Abstract] [Full Text]  

Hidemasa Bono, Itoshi Nikaido, Takeya Kasukawa, Yoshihide Hayashizaki, and Yasushi Okazaki

Comprehensive Analysis of the Mouse Metabolome Based on the Transcriptome
Genome Res. 2003 13: 1345-1349. [Abstract] [Full Text] [Supplemental Research Data]  

Sean M. Grimmond, Kevin C. Miranda, Zheng Yuan, Melissa J. Davis, David A. Hume, Ken Yagi, Naoko Tominaga, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki, and Rohan D. Teasdale

The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment
Genome Res. 2003 13: 1350-1359. [Abstract] [Full Text] [Supplemental Research Data]  

Christine A. Wells, Timothy Ravasi, Razvan Sultana, Ken Yagi, Piero Carninci, Hidemasa Bono, Geoffrey Faulkner, Yasushi Okazaki, John Quackenbush, David A. Hume, and Paul A. Lyons

Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage
Genome Res. 2003 13: 1360-1365. [Abstract] [Full Text] [Supplemental Research Data]  

Alistair R.R. Forrest, Darrin Taylor, and Sean Grimmond

Exploration of the Cell-Cycle Genes Found Within the RIKEN FANTOM2 Data Set
Genome Res. 2003 13: 1366-1375. [Abstract] [Full Text] [Supplemental Research Data]  

John C. Reed, Kutbuddin Doctor, Ana Rojas, Juan M. Zapata, Christian Stehlik, Loredana Fiorentino, Jason Damiano, Wilfried Roth, Shu-ichi Matsuzawa, Ruchi Newman, Shinichi Takayama, Hiroyuki Marusawa, Famming Xu, Guy Salvesen, and Adam Godzik

Comparative Analysis of Apoptosis and Inflammation Genes of Mice and Humans
Genome Res. 2003 13: 1376-1388. [Abstract] [Full Text]  

Colin A.M. Semple, RIKEN GER Group, and GSL Members

The Comparative Proteomics of Ubiquitination in Mouse
Genome Res. 2003 13: 1389-1394. [Abstract] [Full Text]  

Stefano Gustincich, Serge Batalov, Kirk W. Beisel, Hidemasa Bono, Piero Carninci, Colin F. Fletcher, Sean Grimmond, Nobutaka Hirokawa, Erich D. Jarvis, Tim Jegla, Yuka Kawasawa, Julianna LeMieux, Harukata Miki, Elio Raviola, Rohan D. Teasdale, Naoko Tominaga, Ken Yagi, Andreas Zimmer, RIKEN GER Group, GSL Members, Yoshihide Hayashizaki, and Yasushi Okazaki

Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System
Genome Res. 2003 13: 1395-1401. [Abstract] [Full Text] [Supplemental Research Data]  

Itoshi Nikaido, Chika Saito, Yosuke Mizuno, Makiko Meguro, Hidemasa Bono, Moritoshi Kadomura, Tomohiro Kono, Gerard A. Morris, Paul A. Lyons, Mitsuo Oshimura, RIKEN GER Group, GSL Members, Yoshihide Hayashizaki, and Yasushi Okazaki

Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling
Genome Res. 2003 13: 1402-1409. [Abstract] [Full Text]  

Rebecca Holmes, Christine Williamson, Jo Peters, Paul Denny, RIKEN GER Group, GSL Members, and Christine Wells

A Comprehensive Transcript Map of the Mouse Gnas Imprinted Complex
Genome Res. 2003 13: 1410-1415. [Abstract] [Full Text] [Supplemental Research Data]  

Khairina Tajul-Arifin, Rohan Teasdale, Timothy Ravasi, David A. Hume, RIKEN GER Group, GSL Members, and John S. Mattick

Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome
Genome Res. 2003 13: 1416-1429. [Abstract] [Full Text] [Supplemental Research Data]  

Timothy Ravasi, Thomas Huber, Mihaela Zavolan, Alistair Forrest, Terry Gaasterland, Sean Grimmond, RIKEN GER Group, GSL Members, and David A. Hume

Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome
Genome Res. 2003 13: 1430-1442. [Abstract] [Full Text] [Supplemental Research Data]  

Alistair R.R. Forrest, Timothy Ravasi, Darrin Taylor, Thomas Huber, David A. Hume, RIKEN GER Group, GSL Members, and Sean Grimmond

Phosphoregulators: Protein Kinases and Protein Phosphatases of Mouse
Genome Res. 2003 13: 1443-1454. [Abstract] [Full Text] [Supplemental Research Data]  

Harukata Miki, Mitsutoshi Setou, RIKEN GER Group, GSL Members, and Nobutaka Hirokawa

Kinesin Superfamily Proteins (KIFs) in the Mouse Transcriptome
Genome Res. 2003 13: 1455-1465. [Abstract] [Full Text]  

Yuka Kawasawa, Louise M. McKenzie, David P. Hill, Hidemasa Bono, RIKEN GER Group, GSL Members, and Masashi Yanagisawa

G Protein-Coupled Receptor Genes in the FANTOM2 Database
Genome Res. 2003 13: 1466-1477. [Abstract] [Full Text] [Supplemental Research Data]  

Masaaki Furuno, Takeya Kasukawa, Rintaro Saito, Jun Adachi, Harukazu Suzuki, Richard Baldarelli, Yoshihide Hayashizaki, and Yasushi Okazaki

CDS Annotation in Full-Length cDNA Sequence
Genome Res. 2003 13: 1478-1487. [Abstract] [Full Text] [Supplemental Research Data]  

METHODS:

Jun Kawai and Yoshihide Hayashizaki

DNA Book
Genome Res. 2003 13: 1488-1495. [Abstract] [Full Text]  

Lynn M. Schriml, David P. Hill, Judith A. Blake, Hidemasa Bono, Anthony Wynshaw-Boris, William J. Pavan, Brian Z. Ring, Kirk Beisel, Mitsutoshi Setou, RIKEN GER Group, GSL Members, and Yasushi Okazaki

Human Disease Genes and Their Cloned Mouse Orthologs: Exploration of the FANTOM2 cDNA Sequence Data Set
Genome Res. 2003 13: 1496-1500. [Abstract] [Full Text] [Supplemental Research Data]  

RESOURCES:

Boris Lenhard, Claes Wahlestedt, and Wyeth W. Wasserman

GeneLynx Mouse: Integrated Portal to the Mouse Genome
Genome Res. 2003 13: 1501-1504. [Abstract] [Full Text]  

Richard M. Baldarelli, David P. Hill, Judith A. Blake, Jun Adachi, Masaaki Furuno, Dirck Bradt, Lori E. Corbani, Sharon Cousins, Kenneth S. Frazer, Dong Qi, Longlong Yang, Sridhar Ramachandran, Deborah Reed, Yunxia Zhu, Takeya Kasukawa, Martin Ringwald, Benjamin L. King, Lois J. Maltais, Louise M. McKenzie, Lynn M. Schriml, Donna Maglott, Deanna M. Church, Kim Pruitt, Janan T. Eppig, Joel E. Richardson, Jim A. Kadin, and Carol J. Bult

Connecting Sequence and Biology in the Laboratory Mouse
Genome Res. 2003 13: 1505-1519. [Abstract] [Full Text]  

Takeshi Nagashima, Diego G. Silva, Nikolai Petrovsky, Luis A. Socha, Harukazu Suzuki, Rintaro Saito, Takeya Kasukawa, Igor V. Kurochkin, Akihiko Konagaya, and Christian Schönbach

Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS
Genome Res. 2003 13: 1520-1533. [Abstract] [Full Text] [Supplemental Research Data]  

Harukazu Suzuki, Rintaro Saito, Mutsumi Kanamori, Chikatoshi Kai, Christian Schönbach, Takeshi Nagashima, Junko Hosaka, and Yoshihide Hayashizaki

The Mammalian Protein–Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer
Genome Res. 2003 13: 1534-1541. [Abstract] [Full Text]  

Takeya Kasukawa, Masaaki Furuno, Itoshi Nikaido, Hidemasa Bono, David A. Hume, Carol Bult, David P. Hill, Richard Baldarelli, Julian Gough, Alexander Kanapin, Hideo Matsuda, Lynn M. Schriml, Yoshihide Hayashizaki, Yasushi Okazaki, and John Quackenbush

Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
Genome Res. 2003 13: 1542-1551. [Abstract] [Full Text] [Supplemental Research Data]  

ABSTRACTS:

Serge Batalov and Colin F. Fletcher

Exon Structure Analysis, Ortholog Identification, and SNP Candidate Screening by Mapping Mouse RIKEN Sequences to Multiple Genome Assemblies
Genome Res. 2003 13: 1552-1553. [Full Text]  

Hidenori Kiyosawa, Tsugumi Kawashima, Yuki Hasegawa, Itaru Yamanaka, Katsunaga Sakai, Shinji Kondo, RIKEN GER Group, GSL Members, and Yoshihide Hayashizaki

Introduction of RIKEN-GenoMapper, Mapping Viewer System
Genome Res. 2003 13: 1554-1555. [Full Text]  

Serge Batalov, Andrew I. Su, Keith A. Ching, and Colin F. Fletcher

Functional Annotation of RIKEN Mouse cDNA Clones Using GNF Expression Atlas
Genome Res. 2003 13: 1556-1557. [Full Text]  

Yoichi Takenaka and Hideo Matsuda

Analysis of Gene Expression Profiles Based on Clustering
Genome Res. 2003 13: 1558. [Full Text]  

Diego G. Silva, Christian Schönbach, Vladimir Brusic, Luis A. Socha, Takeshi Nagashima, RIKEN GER Group, GSL Members, and Nikolai Petrovsky

Identification of Novel "Pathologs" (Human Disease-Related Gene Candidates) From the RIKEN Full-Length Mouse cDNA Data Set
Genome Res. 2003 13: 1559. [Full Text]  

Igor V. Kurochkin, RIKEN GER Group, GSL Members, Akihiko Konagaya, Takeshi Nagashima, and Christian Schönbach

Identification of Potential Peroxisomal Proteins in Mouse
Genome Res. 2003 13: 1560. [Full Text]  

Yuko Watanabe, Seiji Nishiguchi, Makoto Watanabe, Kazunori Shimada, RIKEN GER Group, GSL Members, Koji Koyama, and Hiromichi Yamanishi

The Mouse Neuronal Protein 15.6 Gene Family
Genome Res. 2003 13: 1561. [Full Text]  

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