PREFACE:
Yoshihide Hayashizaki
Special FANTOM2 Issue
Genome Res. 2003 13: 1265. [Full Text]
http://www.genome.org/cgi/content/full/13/6b/1265
COMMENTARY:
Yasushi Okazaki and David A. Hume
A Guide to the Mammalian Genome
Genome Res. 2003 13: 1267-1272. [Full Text]
http://www.genome.org/cgi/content/full/13/6b/1267
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]
http://www.genome.org/cgi/content/abstract/13/6b/1273
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]
http://www.genome.org/cgi/content/abstract/13/6b/1290
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]
http://www.genome.org/cgi/content/abstract/13/6b/1301
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]
http://www.genome.org/cgi/content/abstract/13/6b/1307
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]
http://www.genome.org/cgi/content/abstract/13/6b/1318
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]
http://www.genome.org/cgi/content/abstract/13/6b/1324
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]
http://www.genome.org/cgi/content/abstract/13/6b/1335
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]
http://www.genome.org/cgi/content/abstract/13/6b/1345
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]
http://www.genome.org/cgi/content/abstract/13/6b/1350
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]
http://www.genome.org/cgi/content/abstract/13/6b/1360
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]
http://www.genome.org/cgi/content/abstract/13/6b/1366
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]
http://www.genome.org/cgi/content/abstract/13/6b/1376
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]
http://www.genome.org/cgi/content/abstract/13/6b/1389
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]
http://www.genome.org/cgi/content/abstract/13/6b/1395
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]
http://www.genome.org/cgi/content/abstract/13/6b/1402
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]
http://www.genome.org/cgi/content/abstract/13/6b/1410
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]
http://www.genome.org/cgi/content/abstract/13/6b/1416
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]
http://www.genome.org/cgi/content/abstract/13/6b/1430
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]
http://www.genome.org/cgi/content/abstract/13/6b/1443
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]
http://www.genome.org/cgi/content/abstract/13/6b/1455
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]
http://www.genome.org/cgi/content/abstract/13/6b/1466
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]
http://www.genome.org/cgi/content/abstract/13/6b/1478
METHODS:
Jun Kawai and Yoshihide Hayashizaki
DNA Book
Genome Res. 2003 13: 1488-1495. [Abstract]
[Full Text]
http://www.genome.org/cgi/content/abstract/13/6b/1488
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]
http://www.genome.org/cgi/content/abstract/13/6b/1496
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]
http://www.genome.org/cgi/content/abstract/13/6b/1501
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]
http://www.genome.org/cgi/content/abstract/13/6b/1505
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]
http://www.genome.org/cgi/content/abstract/13/6b/1520
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]
http://www.genome.org/cgi/content/abstract/13/6b/1534
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]
http://www.genome.org/cgi/content/abstract/13/6b/1542
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]
http://www.genome.org/cgi/content/full/13/6b/1552
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]
http://www.genome.org/cgi/content/full/13/6b/1554
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]
http://www.genome.org/cgi/content/full/13/6b/1556
Yoichi Takenaka and Hideo Matsuda
Analysis of Gene Expression Profiles Based
on Clustering
Genome Res. 2003 13: 1558. [Full Text]
http://www.genome.org/cgi/content/full/13/6b/1558
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]
http://www.genome.org/cgi/content/full/13/6b/1559
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]
http://www.genome.org/cgi/content/full/13/6b/1560
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]
http://www.genome.org/cgi/content/full/13/6b/1561
COVER CAPTION:
Cover The illustration symbolizes the "RIKEN Mouse Genome Encyclopedia"
project: the whole system
from mouse house to database. The left photo is the BK6 mouse used for
sequencing in this project. The
yellow cup below it represents the RISA system (RIKEN Integrated Sequence
Analyzer). Data output is
delivered and stored in a PC, and clones are stored as printed material
as in the "DNA Book" in this
issue. The right photo is the FANTOM2 collaborative members at the Cherry
Blossom Meeting held by RIKEN
GSC in 2002. (Cover designed by Dr. Chie Owa; For details, see Kawai et
al., pp. 1488-1495.)
http://www.genome.org/cgi/content/short/13/6b/1488
1. Saha S, Ansari AZ, Jarell KA, and Ptashne M, "RNA Sequences that Work as Transcriptional Activating Regions".
2. Lee JM, and Sonnhammer ELL, "Genomic Gene Clustering Analysis of Pathways in Eukaryotes".
3. Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL, Duke K, Kiraly M, and Kim SK, "A Global Analysis of Caenorhabditis elegans Operons".
4. Storz G, "An Expanding Universe of Noncoding RNAs".
5. Eddy SR, "Non-Coding RNA Genes and the Modern RNA World".
6. Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H, Bachellerie J-P, and Brosius J, "RNomics: An Experimental Approach that Identifies 201 Candidates for Novel, Small, Non-Messenger RNAs in Mouse".
7. Hovsepian JA, and Frenster JH, "RNA-Induced Melting of DNA during Selective Gene Transcription".
8. Frenster JH, "Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".
9. Special Issue of Genome Research, vol. 13,
no. 6b, pp. 1265-1561 (June 2, 2003).
Report of "RIKEN Mouse Genome Encyclopedia" project: the whole system
from mouse house to database.