The Genome Network Project/FANTOM3 Collection in PLoS Genetics

: 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.

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Editorial

Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome: Hayashizaki Y, Carninci P; doi:10.1371/journal.pgen.0020063

Technical Report

Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs: Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, et al.; doi:10.1371/journal.pgen.0020062

Research Articles

Pseudo-Messenger RNA: Phantoms of the Transcriptome: Frith MC, Wilming LG, Forrest A, Kawaji H, Tan SL, et al.; doi:10.1371/journal.pgen.0020023
The Abundance of Short Proteins in the Mammalian Proteome: Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, et al.; doi:10.1371/journal.pgen.0020052
Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines: Liu J, Gough J, Rost B; doi:10.1371/journal.pgen.0020029
Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs: Furuno M, Pang KC, Ninomiya N, Fukuda S, Frith MC, et al.; doi:10.1371/journal.pgen.0020037
Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units: Davis MJ, Hanson KA, Clark F, Fink JL, Zhang F, et al.; doi:10.1371/journal.pgen.0020046
Complex Loci in Human and Mouse Genomes: Engström PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, et al.; doi:10.1371/journal.pgen.0020047
A Method for Similarity Search of Genomic Positional Expression Using CAGE: Seno S, Takenaka Y, Kai C, Kawai J, Carninci P, et al.; doi:10.1371/journal.pgen.0020044
SPA: A Probabilistic Algorithm for Spliced Alignment: van Nimwegen E, Paul N, Sheridan R, Zavolan M; doi:10.1371/journal.pgen.0020024
A Simple Physical Model Predicts Small Exon Length Variations: Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, et al.; doi:10.1371/journal.pgen.0020045
Mice and Men: Their Promoter Properties: Bajic VB, Tan SL, Christoffels A, Schönbach C, Lipovich L, et al.; doi:10.1371/journal.pgen.0020054
Heterotachy in Mammalian Promoter Evolution: Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, et al.; doi:10.1371/journal.pgen.0020030