Biology & Life Sciences

The Genome Network Project/FANTOM3 Collection

Published June 8, 2016 Partnered Collections, Special Issues

The Genome Network Project/FANTOM3 collection features articles describing findings that redefine the landscape of the mammalian transcriptome by introducing an extensive collection of novel cDNAs and millions of sequenced tags corresponding to 5'- and 3'-ends of mRNAs. The high-resolution cDNA collection and its analysis represent an important world resource for discovery, and demonstrate the value of large-scale transcriptome approaches toward understanding genome function.

Image Credit: Melissa Garden Streblow

Jump to section

Editorial
Technical Report
Research Articles

Editorial

Image credit
10.1371/journal.pgen.0020063

PLOS Genetics Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome
April 28, 2006 Yoshihide Hayashizaki, Piero Carninci

Technical Report

Image credit
10.1371/journal.pgen.0020062

PLOS Genetics Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs
April 28, 2006 Norihiro Maeda, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin Frith, Pär G Engström, Boris Lenhard, Rajith N Aturaliya, Serge Batalov, Kirk W Beisel, Carol J Bult, Colin F Fletcher, Alistair R. R Forrest, Masaaki Furuno, David Hill, Masayoshi Itoh, Mutsumi Kanamori-Katayama, Shintaro Katayama, Masaru Katoh, Tsugumi Kawashima, John Quackenbush, Timothy Ravasi, Brian Z Ring, Kazuhiro Shibata, Koji Sugiura, Yoichi Takenaka, Rohan D Teasdale, Christine A Wells, Yunxia Zhu, Chikatoshi Kai, Jun Kawai, David A Hume, Piero Carninci, Yoshihide Hayashizaki

Research Articles

Image credit
10.1371/journal.pgen.0020023

PLOS Genetics Pseudo–Messenger RNA: Phantoms of the Transcriptome
April 28, 2006 Martin C Frith, Laurens G Wilming, Alistair Forrest, Hideya Kawaji, Sin Lam Tan, Claes Wahlestedt, Vladimir B Bajic, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Timothy L Bailey, Lukasz Huminiecki
Image credit
10.1371/journal.pgen.0020052

PLOS Genetics The Abundance of Short Proteins in the Mammalian Proteome
April 28, 2006 Martin C Frith, Alistair R Forrest, Ehsan Nourbakhsh, Ken C Pang, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Timothy L Bailey, Sean M Grimmond
Image credit
10.1371/journal.pgen.0020029

PLOS Genetics Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines
April 28, 2006 Jinfeng Liu, Julian Gough, Burkhard Rost
Image credit
10.1371/journal.pgen.0020037

PLOS Genetics Clusters of Internally Primed Transcripts Reveal Novel Long NoncodingRNAs
April 28, 2006 Masaaki Furuno, Ken C Pang, Noriko Ninomiya, Shiro Fukuda, Martin C Frith, Carol Bult, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, John S Mattick, Harukazu Suzuki
Image credit
10.1371/journal.pgen.0020046

PLOS Genetics Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units
April 28, 2006 Melissa J Davis, Kelly A Hanson, Francis Clark, J. Lynn Fink, Fasheng Zhang, Takeya Kasukawa, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Rohan D Teasdale
Image credit
10.1371/journal.pgen.0020047

PLOS Genetics Complex Loci in Human and Mouse Genomes
April 28, 2006 Pär G Engström, Harukazu Suzuki, Noriko Ninomiya, Altuna Akalin, Luca Sessa, Giovanni Lavorgna, Alessandro Brozzi, Lucilla Luzi, Sin Lam Tan, Liang Yang, Galih Kunarso, Edwin Lian-Chong Ng, Serge Batalov, Claes Wahlestedt, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Christine Wells, Vladimir B Bajic, Valerio Orlando, James F Reid, Boris Lenhard, Leonard Lipovich
Image credit
10.1371/journal.pgen.0020044

PLOS Genetics A Method for Similarity Search of Genomic Positional Expression UsingCAGE
April 28, 2006 Shigeto Seno, Yoichi Takenaka, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Hideo Matsuda
Image credit
10.1371/journal.pgen.0020024

PLOS Genetics SPA: A Probabilistic Algorithm for Spliced Alignment
April 28, 2006 Erik van Nimwegen, Nicodeme Paul, Robert Sheridan, Mihaela Zavolan
Image credit
10.1371/journal.pgen.0020045

PLOS Genetics A Simple Physical Model Predicts Small Exon Length Variations
April 28, 2006 Tzu-Ming Chern, Erik van Nimwegen, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Mihaela Zavolan
Image credit
10.1371/journal.pgen.0020054

PLOS Genetics Mice and Men: Their Promoter Properties
April 28, 2006 Vladimir B Bajic, Sin Lam Tan, Alan Christoffels, Christian Schönbach, Leonard Lipovich, Liang Yang, Oliver Hofmann, Adele Kruger, Winston Hide, Chikatoshi Kai, Jun Kawai, David A Hume, Piero Carninci, Yoshihide Hayashizaki
Image credit
Melissa Garden Streblow

PLOS Genetics Heterotachy in Mammalian Promoter Evolution
April 28, 2006 Martin S Taylor, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Colin A. M Semple

Collection Editors

Judith A. Blake (The Jackson Laboratory), Wayne N. Frankel (The Jackson Laboratory), John M. Hancock (MRC Harwell), William J. Pavan (National Human Genome Research Institute), and Lisa Stubbs (University of Illinois at Urbana-Champaign)

PLOS Collections Blog - Biology & Life Sciences