Table of Contents

June 2003; 13 (6b)

Preface

COMMENTARY

  • A Guide to the Mammalian Genome

    • Yasushi Okazaki and
    • David A. Hume
    Genome Res. June 2003 13: 1267-1272; doi:10.1101/gr.1445603

ARTICLES

  • Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

    • 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
    Genome Res. June 2003 13: 1273-1289; doi:10.1101/gr.1119703

  • Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome

    • Mihaela Zavolan,
    • Shinji Kondo,
    • Christian Schönbach,
    • Jun Adachi,
    • David A. Hume,
    • RIKEN GER Group,
    • GSL Members,
    • Yoshihide Hayashizaki,
    • and Terry Gaasterland
    Genome Res. June 2003 13: 1290-1300; doi:10.1101/gr.1017303

  • Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection

    • 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
    Genome Res. June 2003 13: 1301-1306; doi:10.1101/gr.1011603

  • Cytokine-Related Genes Identified From the RIKEN Full-Length Mouse cDNA Data Set

    • Vladimir Brusic,
    • Rekha S. Pillai,
    • Diego G. Silva,
    • Nikolai Petrovsky,
    • RIKEN GER Group,
    • GSL Members,
    • and Christian Schönbach
    Genome Res. June 2003 13: 1307-1317; doi:10.1101/gr.1016503

LETTERS

  • Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays

    • 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,
    • RIKEN GER Group,
    • GSL Members,
    • Yoshihide Hayashizaki,
    • and Yasushi Okazaki
    Genome Res. June 2003 13: 1318-1323; doi:10.1101/gr.1075103

  • Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation

    • Hidenori Kiyosawa,
    • Itaru Yamanaka,
    • Naoki Osato,
    • Shinji Kondo,
    • RIKEN GER Group,
    • GSLMembers,
    • and Yoshihide Hayashizaki
    Genome Res. June 2003 13: 1324-1334; doi:10.1101/gr.982903

  • Mouse Proteome Analysis

    • Alexander Kanapin,
    • Serge Batalov,
    • Melissa J. Davis,
    • Julian Gough,
    • Sean Grimmond,
    • Hideya Kawaji,
    • Michele Magrane,
    • Hideo Matsuda,
    • Christian Schönbach,
    • Rohan D. Teasdale,
    • RIKEN GER Group,
    • GSL Members,
    • and Zheng Yuan3
    Genome Res. June 2003 13: 1335-1344; doi:10.1101/gr.978703

  • Comprehensive Analysis of the Mouse Metabolome Based on the Transcriptome

    • Hidemasa Bono,
    • Itoshi Nikaido,
    • Takeya Kasukawa,
    • RIKEN GER Group,
    • GSL Members,
    • Yoshihide Hayashizaki,
    • and Yasushi Okazaki
    Genome Res. June 2003 13: 1345-1349; doi:10.1101/gr.974603

  • The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment

    • Sean M. Grimmond,
    • Kevin C. Miranda,
    • Zheng Yuan,
    • Melissa J. Davis,
    • David A. Hume,
    • Ken Yagi,
    • Naoko Tominaga,
    • Hidemasa Bono,
    • Yoshihide Hayashizaki,
    • Yasushi Okazaki,
    • RIKEN GER Group,
    • GSL Members,
    • and Rohan D. Teasdale
    Genome Res. June 2003 13: 1350-1359; doi:10.1101/gr.983703

  • Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage

    • Christine A. Wells,
    • Timothy Ravasi,
    • Razvan Sultana,
    • Ken Yagi,
    • Piero Carninci,
    • Hidemasa Bono,
    • Geoffrey Faulkner,
    • Yasushi Okazaki,
    • John Quackenbush,
    • David A. Hume,
    • RIKEN GER Group,
    • GSL Members,
    • and Paul A. Lyons
    Genome Res. June 2003 13: 1360-1365; doi:10.1101/gr.1056103

  • Exploration of the Cell-Cycle Genes Found Within the RIKEN FANTOM2 Data Set

    • Alistair R.R. Forrest,
    • Darrin Taylor,
    • RIKEN GER Group,
    • GSL Members,
    • and Sean Grimmond
    Genome Res. June 2003 13: 1366-1375; doi:10.1101/gr.1012403

  • Comparative Analysis of Apoptosis and Inflammation Genes of Mice and Humans

    • 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,
    • RIKEN GER Group,
    • GSL Members,
    • and Adam Godzik
    Genome Res. June 2003 13: 1376-1388; doi:10.1101/gr.1053803

  • The Comparative Proteomics of Ubiquitination in Mouse

    • Colin A.M. Semple,
    • RIKEN GER Group,
    • and GSL Members
    Genome Res. June 2003 13: 1389-1394; doi:10.1101/gr.980303

  • Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System

    • 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
    Genome Res. June 2003 13: 1395-1401; doi:10.1101/gr.1135303

  • Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling

    • 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
    Genome Res. June 2003 13: 1402-1409; doi:10.1101/gr.1055303

  • A Comprehensive Transcript Map of the Mouse Gnas Imprinted Complex

    • Rebecca Holmes,
    • Christine Williamson,
    • Jo Peters,
    • Paul Denny,
    • RIKEN GER Group,
    • GSL Members,
    • and Christine Wells
    Genome Res. June 2003 13: 1410-1415; doi:10.1101/gr.955503

  • Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome

    • Khairina Tajul-Arifin,
    • Rohan Teasdale,
    • Timothy Ravasi,
    • David A. Hume,
    • RIKEN GER Group,
    • GSL Members,
    • and John S. Mattick
    Genome Res. June 2003 13: 1416-1429; doi:10.1101/gr.1015703

  • Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome

    • Timothy Ravasi,
    • Thomas Huber,
    • Mihaela Zavolan,
    • Alistair Forrest,
    • Terry Gaasterland,
    • Sean Grimmond,
    • RIKEN GER Group,
    • GSL Members,
    • and David A. Hume
    Genome Res. June 2003 13: 1430-1442; doi:10.1101/gr.949803

  • Phosphoregulators: Protein Kinases and Protein Phosphatases of Mouse

    • Alistair R.R. Forrest,
    • Timothy Ravasi,
    • Darrin Taylor,
    • Thomas Huber,
    • David A. Hume,
    • RIKEN GER Group,
    • GSL Members,
    • and Sean Grimmond
    Genome Res. June 2003 13: 1443-1454; doi:10.1101/gr.954803

  • Kinesin Superfamily Proteins (KIFs) in the Mouse Transcriptome

    • Harukata Miki,
    • Mitsutoshi Setou,
    • RIKEN GER Group,
    • GSL Members,
    • and Nobutaka Hirokawa
    Genome Res. June 2003 13: 1455-1465; doi:10.1101/gr.984503

  • G Protein-Coupled Receptor Genes in the FANTOM2 Database

    • Yuka Kawasawa,
    • Louise M. McKenzie,
    • David P. Hill,
    • Hidemasa Bono,
    • RIKEN GER Group,
    • GSL Members,
    • and Masashi Yanagisawa
    Genome Res. June 2003 13: 1466-1477; doi:10.1101/gr.1087603

  • CDS Annotation in Full-Length cDNA Sequence

    • Masaaki Furuno,
    • Takeya Kasukawa,
    • Rintaro Saito,
    • Jun Adachi,
    • Harukazu Suzuki,
    • Richard Baldarelli,
    • Yoshihide Hayashizaki,
    • and Yasushi Okazaki
    Genome Res. June 2003 13: 1478-1487; doi:10.1101/gr.1060303

Methods

  • DNA Book

    • Jun Kawai and
    • Yoshihide Hayashizaki
    Genome Res. June 2003 13: 1488-1495; doi:10.1101/gr.914203

  • Human Disease Genes and Their Cloned Mouse Orthologs: Exploration of the FANTOM2 cDNA Sequence Data Set

    • 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
    Genome Res. June 2003 13: 1496-1500; doi:10.1101/gr.979503

RESOURCES

  • GeneLynx Mouse: Integrated Portal to the Mouse Genome

    • Boris Lenhard,
    • Claes Wahlestedt,
    • and Wyeth W. Wasserman
    Genome Res. June 2003 13: 1501-1504; doi:10.1101/gr.951403

  • Connecting Sequence and Biology in the Laboratory Mouse

    • 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
    Genome Res. June 2003 13: 1505-1519; doi:10.1101/gr.991003

  • Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS

    • Takeshi Nagashima,
    • Diego G. Silva,
    • Nikolai Petrovsky,
    • Luis A. Socha,
    • Harukazu Suzuki,
    • Rintaro Saito,
    • Takeya Kasukawa,
    • Igor V. Kurochkin,
    • Akihiko Konagaya,
    • and Christian Schönbach
    Genome Res. June 2003 13: 1520-1533; doi:10.1101/gr.1019903

  • The Mammalian Protein–Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer

    • Harukazu Suzuki,
    • Rintaro Saito,
    • Mutsumi Kanamori,
    • Chikatoshi Kai,
    • Christian Schönbach,
    • Takeshi Nagashima,
    • Junko Hosaka,
    • and Yoshihide Hayashizaki
    Genome Res. June 2003 13: 1534-1541; doi:10.1101/gr.956303

  • Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System

    • 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
    Genome Res. June 2003 13: 1542-1551; doi:10.1101/gr.992803

Abstracts

  • Exon Structure Analysis, Ortholog Identification, and SNP Candidate Screening by Mapping Mouse RIKEN Sequences to Multiple Genome Assemblies

    • Serge Batalov and
    • Colin F. Fletcher
    Genome Res. June 2003 13: 1552-1553; doi:10.1101/gr.1458903

  • Introduction of RIKEN-GenoMapper, Mapping Viewer System

    • Hidenori Kiyosawa,
    • Tsugumi Kawashima,
    • Yuki Hasegawa,
    • Itaru Yamanaka,
    • Katsunaga Sakai,
    • Shinji Kondo,
    • RIKEN GER Group,
    • GSL Members,
    • and Yoshihide Hayashizaki
    Genome Res. June 2003 13: 1554-1555; doi:10.1101/gr.1462103

  • Functional Annotation of RIKEN Mouse cDNA Clones Using GNF Expression Atlas

    • Serge Batalov,
    • Andrew I. Su,
    • Keith A. Ching,
    • and Colin F. Fletcher
    Genome Res. June 2003 13: 1556-1557; doi:10.1101/gr.1457103

  • Analysis of Gene Expression Profiles Based on Clustering

    • Yoichi Takenaka and
    • Hideo Matsuda
    Genome Res. June 2003 13: 1558; doi:10.1101/gr.1459703

  • Identification of Novel “Pathologs” (Human Disease-Related Gene Candidates) From the RIKEN Full-Length Mouse cDNA Data Set

    • Diego G. Silva,
    • Christian Schönbach,
    • Vladimir Brusic,
    • Luis A. Socha,
    • Takeshi Nagashima,
    • RIKEN GER Group,
    • GSL Members,
    • and Nikolai Petrovsky
    Genome Res. June 2003 13: 1559; doi:10.1101/gr.1461303

  • Identification of Potential Peroxisomal Proteins in Mouse

    • Igor V. Kurochkin,
    • RIKEN GER Group,
    • GSL Members,
    • Akihiko Konagaya,
    • Takeshi Nagashima,
    • and Christian Schönbach
    Genome Res. June 2003 13: 1560; doi:10.1101/gr.1456303

  • The Mouse Neuronal Protein 15.6 Gene Family

    • Yuko Watanabe,
    • Seiji Nishiguchi,
    • Makoto Watanabe,
    • Kazunori Shimada,
    • RIKEN GER Group,
    • GSL Members,
    • Koji Koyama,
    • and Hiromichi Yamanishi
    Genome Res. June 2003 13: 1561; doi:10.1101/gr.1460503
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This Issue

June 2003; 13 (6b)
Cover
  1. Preface
  2. COMMENTARY
  3. ARTICLES
  4. LETTERS
  5. Methods
  6. RESOURCES
  7. Abstracts

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