Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.
Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.
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DOI：
10.1093/nar/gki711
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发表时间：
2005
影响因子：
14.9
通讯作者：
Karp PD
中科院分区：
文献类型：
--
作者：
Green ML;Karp PD
我们报告了基因组和途径数据库中一种新型的系统注释错误，它是由于对部分酶委员会(EC)编号的误解而导致的，如‘1.1.1.-’。这个错误导致用部分EC编号标注的基因被分配给用相同的部分EC编号标注的许多或所有生化反应。这一推论是错误的，因为部分EC数字具有模棱两可的性质。我们在包括KEGG、VIMSS和IMG在内的多个数据库中观察到了这种类型的错误，所有这些数据库都将基因分配给KEGG途径。KEGG数据库的大肠杆菌子集在其6.8%的基因反应分配中显示了这一错误。例如，KEGG包含17个用EC 1.1.1注释的反应。一组三个大肠杆菌基因b1580[假定的脱氢酶，NAD(P)结合，饥饿敏感蛋白]，b3787(UDP-N-乙酰-d-甘露糖醛酸脱氢酶)和b0207(2，5-二酮-d-葡萄糖酸还原酶B)被归类于其中的15个反应，尽管实验证据表明这三个基因中的两个具有不同的单一功能。此外，数据库(DB)在内部是不一致的，因为对具有部分EC编号的基因的基因功能的描述与这些基因被分配到的反应所暗示的活动不一致。我们推断，这些不一致的原因是用于将基因产品与KEGG代谢途径中的反应相匹配的处理。这些错误影响了使用这些数据库作为在线百科全书的科学家，也影响了使用这些数据库训练和验证新开发的算法的生物信息学家。
We report on a new type of systematic annotation error in genome and pathway databases that results from the misinterpretation of partial Enzyme Commission (EC) numbers such as ‘1.1.1.-’. This error results in the assignment of genes annotated with a partial EC number to many or all biochemical reactions that are annotated with the same partial EC number. That inference is faulty because of the ambiguous nature of partial EC numbers. We have observed this type of error in multiple databases, including KEGG, VIMSS and IMG, all of which assign genes to KEGG pathways. The Escherichia coli subset of the KEGG database exhibits this error for 6.8% of its gene-reaction assignments. For example, KEGG contains 17 reactions that are annotated with EC 1.1.1.-. A group of three E.coli genes, b1580 [putative dehydrogenase, NAD(P)-binding, starvation-sensing protein], b3787 (UDP-N-acetyl-d-mannosaminuronic acid dehydrogenase) and b0207 (2,5-diketo-d-gluconate reductase B), is assigned to 15 of those reactions, despite experimental evidence indicating different single functions for two of the three genes. Furthermore, the databases (DBs) are internally inconsistent in that the description of gene functions for genes with partial EC numbers is inconsistent with the activities implied by reactions to which the genes were assigned. We infer that these inconsistencies result from the processing used to match gene products to reactions within KEGG's metabolic pathways. These errors affect scientists who use these DBs as online encyclopedias and they affect bioinformaticists who use these DBs to train and validate newly developed algorithms.
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影响因子：
3.2
作者：
Eichler, K;Buchet, A;MandrandBerthelot, MA
通讯作者：
MandrandBerthelot, MA
影响因子：
14.9
作者：
Keseler IM;Collado-Vides J;Gama-Castro S;Ingraham J;Paley S;Paulsen IT;Peralta-Gil M;Karp PD
通讯作者：
Karp PD
影响因子：
5.8
作者：
Wu, J;Kasif, S;DeLisi, C
通讯作者：
DeLisi, C
影响因子：
14.9
作者：
Kanehisa, M;Goto, S;Hattori, M
通讯作者：
Hattori, M
影响因子：
11.4
作者：
Yanai, I;Mellor, JC;DeLisi, C
通讯作者：
DeLisi, C