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 annotati...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2006-04-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC1449903?pdf=render |
| _version_ | 1828486118170951680 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Norihiro Maeda |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T09:27:31Z |
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| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-11T09:27:31Z |
| publishDate | 2006-04-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS Genetics |
| spelling | doaj.art-715f2767f50e469fbc189398f0eb0f8f2022-12-22T01:13:06ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042006-04-0124e6210.1371/journal.pgen.0020062Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.Norihiro MaedaTakeya KasukawaRieko OyamaJulian GoughMartin FrithPär G EngströmBoris LenhardRajith N AturaliyaSerge BatalovKirk W BeiselCarol J BultColin F FletcherAlistair R R ForrestMasaaki FurunoDavid HillMasayoshi ItohMutsumi Kanamori-KatayamaShintaro KatayamaMasaru KatohTsugumi KawashimaJohn QuackenbushTimothy RavasiBrian Z RingKazuhiro ShibataKoji SugiuraYoichi TakenakaRohan D TeasdaleChristine A WellsYunxia ZhuChikatoshi KaiJun KawaiDavid A HumePiero CarninciYoshihide HayashizakiThe 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.http://europepmc.org/articles/PMC1449903?pdf=render |
| spellingShingle | 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 Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genetics |
| title | Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. |
| title_full | Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. |
| title_fullStr | Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. |
| title_full_unstemmed | Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. |
| title_short | Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. |
| title_sort | transcript annotation in fantom3 mouse gene catalog based on physical cdnas |
| url | http://europepmc.org/articles/PMC1449903?pdf=render |
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