GENCODE: producing a reference annotation for ENCODE.
GENCODE: producing a reference annotation for ENCODE.
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DOI：
10.1186/gb-2006-7-s1-s4
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发表时间：
2006
期刊：
影响因子：
12.3
通讯作者：
Guigo R
中科院分区：
文献类型：
--
作者：
Harrow J;Denoeud F;Frankish A;Reymond A;Chen CK;Chrast J;Lagarde J;Gilbert JG;Storey R;Swarbreck D;Rossier C;Ucla C;Hubbard T;Antonarakis SE;Guigo R
GENCODE联盟的成立是为了识别和绘制ENCODE区域内所有的蛋白质编码基因。这是通过哈瓦那团队最初的手动注释、GENCODE联盟的实验验证以及基于这些实验结果对注释的完善相结合来实现的。
GENCODE基因特征分为八个不同类别，其中只有前两类（已知的和新的编码序列）被有把握地预测为蛋白质编码基因。5' cDNA末端快速扩增（RACE）和逆转录聚合酶链反应（RT - PCR）被用于对初始注释进行实验验证。在测试的420个编码位点中，229个RACE产物已被测序。它们支持了30个位点的5'延伸以及50个位点的新剪接变体。此外，46个没有编码序列证据的位点得到了验证，其中包括31个新的和15个假定的转录本。我们通过尝试验证GENCODE注释之外的所有预测外显子边界来评估GENCODE注释的全面性。在ENCODE区域的一个子集中测试的1215个外显子边界中，14个新的外显子对得到了验证，其中只有两个位于基因间区域。
总共有487个位点，其中434个是编码位点，已作为可从加州大学圣克鲁兹分校（UCSC）浏览器获取的GENCODE参考集的一部分进行了注释。GENCODE注释与RefSeq和ENSEMBL的比较表明，只有40%的GENCODE外显子包含在这两个集合中，这反映了所注释的具有独特外显子的可变剪接形式数量众多。超过50%的编码位点已通过针对EGASP的5' RACE进行了实验验证，并且GENCODE合作项目正在借助实验验证继续完善其对1%人类基因组的注释。
The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.
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影响因子：
7.7
作者：
Mattick, JS
通讯作者：
Mattick, JS
DOI：
10.1073/pnas.0337561100
发表时间：
2003-02-04
影响因子：
11.1
作者：
Guigó, R;Dermitzakis, ET;Brent, MR
通讯作者：
Brent, MR
影响因子：
4.3
作者：
Ohler U;Shomron N;Burge CB
通讯作者：
Burge CB
影响因子：
64.8
作者：
Deloukas, P;Matthews, LH;Rogers, J
通讯作者：
Rogers, J
影响因子：
7
作者：
Down, TA;Hubbard, TJP
通讯作者：
Hubbard, TJP