Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of cDNAs still remained to be collected and identified. To pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full-length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web-based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full-length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding (including partial or truncated transcripts), providing to our knowledge the greatest current coverage of the mouse proteome by full-length cDNAs. The total number of distinct non-protein-coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and final expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species.
Maeda
Norihiro
N
Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan. rgscerg@gsc.riken.jp
Kasukawa
Takeya
T
Oyama
Rieko
R
Gough
Julian
J
Frith
Martin
M
Engström
Pär G
PG
Lenhard
Boris
B
Aturaliya
Rajith N
RN
Batalov
Serge
S
Beisel
Kirk W
KW
Bult
Carol J
CJ
Fletcher
Colin F
CF
Forrest
Alistair R R
AR
Furuno
Masaaki
M
Hill
David
D
Itoh
Masayoshi
M
Kanamori-Katayama
Mutsumi
M
Katayama
Shintaro
S
Katoh
Masaru
M
Kawashima
Tsugumi
T
Quackenbush
John
J
Ravasi
Timothy
T
Ring
Brian Z
BZ
Shibata
Kazuhiro
K
Sugiura
Koji
K
Takenaka
Yoichi
Y
Teasdale
Rohan D
RD
Wells
Christine A
CA
Zhu
Yunxia
Y
Kai
Chikatoshi
C
Kawai
Jun
J
Hume
David A
DA
Carninci
Piero
P
Hayashizaki
Yoshihide
Y