EGASP: the human ENCODE Genome Annotation Assessment Project.
EGASP: the human ENCODE Genome Annotation Assessment Project.
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DOI：
10.1186/gb-2006-7-s1-s2
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发表时间：
2006
期刊：
影响因子：
12.3
通讯作者：
Reese MG
中科院分区：
文献类型：
--
作者：
Guigó R;Flicek P;Abril JF;Reymond A;Lagarde J;Denoeud F;Antonarakis S;Ashburner M;Bajic VB;Birney E;Castelo R;Eyras E;Ucla C;Gingeras TR;Harrow J;Hubbard T;Lewis SE;Reese MG
我们介绍了EGASP的结果，EGASP是一个社区实验，旨在评估ENCODE区域内基因组注释的最新技术水平，该区域跨越人类基因组序列的1%。该实验有两个主要目标：评估预测蛋白质编码基因的计算方法的准确性;以及全面评估ENCODE区域所代表的当前人类基因组注释的完整性。对于计算预测评估，18个组贡献了基因预测。我们根据GENCODE项目生成的注释的"参考集"对这些提交的文件进行了评估。这些注释在提交截止日期之前无法提供给预测小组，因此他们的预测是盲目的，外部咨询委员会可以进行公平的评估。最好的方法至少有一个基因转录正确预测近70%的注释基因。然而，考虑到可变剪接，多重转录准确度仅达到约40%至50%的准确度。在编码核苷酸水平上，最好的程序在敏感性和特异性方面均达到90%的准确性。依赖于mRNA和蛋白质序列的程序在复制手动管理的注释方面是最准确的。实验验证表明，只有一个非常小的百分比（3.2%）的选定的221个计算预测的外显子以外的现有注释可以验证。这是第一次在人类DNA中进行这样的实验，我们遵循了在果蝇中进行的类似实验GASP 1中建立的标准。我们相信，这里提出的结果有助于正在进行的大规模注释项目的价值，并应指导进一步的实验方法时，扩大到整个人类基因组序列。
We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.
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影响因子：
56.9
作者：
Cheng, J;Kapranov, P;Gingeras, TR
通讯作者：
Gingeras, TR
影响因子：
14.9
作者：
Castelo, R;Reymond, A;Wyss, C;Câmara, F;Parra, G;Antonarakis, SE;Guigó, R;Eyras, E
通讯作者：
Eyras, E
影响因子：
7
作者：
Collins, JE;Goward, ME;Dunham, I
通讯作者：
Dunham, I
影响因子：
7
作者：
Curwen, V;Eyras, E;Clamp, M
通讯作者：
Clamp, M
影响因子：
7
作者：
Alexandersson, M;Cawley, S;Pachter, L
通讯作者：
Pachter, L