Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
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DOI：
10.1371/journal.pgen.0020062
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发表时间：
2006-04
期刊：
影响因子：
4.5
通讯作者：
Hayashizaki Y
中科院分区：
文献类型：
--
作者：
Maeda N;Kasukawa T;Oyama R;Gough J;Frith M;Engström PG;Lenhard B;Aturaliya RN;Batalov S;Beisel KW;Bult CJ;Fletcher CF;Forrest AR;Furuno M;Hill D;Itoh M;Kanamori-Katayama M;Katayama S;Katoh M;Kawashima T;Quackenbush J;Ravasi T;Ring BZ;Shibata K;Sugiura K;Takenaka Y;Teasdale RD;Wells CA;Zhu Y;Kai C;Kawai J;Hume DA;Carninci P;Hayashizaki Y
国际FANTOM联盟旨在基于广泛的cDNA收集以及对全长富集cDNA的功能注释，绘制出哺乳动物转录组的全貌。之前的数据集FANTOM2包含60770个全长富集cDNA。功能注释显示，该cDNA数据集仅包含约一半估计数量的小鼠蛋白质编码基因，这表明仍有许多cDNA有待收集和鉴定。为了获得涵盖所有预测小鼠基因的完整基因目录，自FANTOM2以来，全长富集cDNA的克隆和测序一直在继续。在FANTOM3中，对42031个新分离的cDNA进行了功能注释，并更新了4347个FANTOM2 cDNA的注释。为了实现准确的功能注释，我们通过引入新的编码序列预测程序改进了自动化注释流程，并开发了一个基于网络的注释界面，以简化注释程序，减少人工注释错误。自动化的编码序列和功能预测之后，由专家编审进行人工编审和审核。总共对102801个全长富集的小鼠cDNA进行了注释。在102801个转录本中，56722个被功能注释为蛋白质编码（包括部分或截短的转录本），据我们所知，这是目前全长cDNA对小鼠蛋白质组覆盖最广的一次。不同的非蛋白质编码转录本总数增加到34030个。FANTOM3注释系统由自动化计算预测、人工编审和最终的专家编审组成，促进了对小鼠转录组的全面表征，并可应用于其他物种的转录组。
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.
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
14.9
作者：
Pang, KC;Stephen, S;Mattick, JS
通讯作者：
Mattick, JS
影响因子：
7
作者：
Stein, LD;Mungall, C;Lewis, S
通讯作者：
Lewis, S
影响因子：
4.6
作者：
Fukunishi, Y;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
14.9
作者：
Blake, JA;Richardson, JE;Eppig, JT
通讯作者：
Eppig, JT