MedicCyc:: a biochemical pathway database for Medicago truncatula
MedicCyc:: a biochemical pathway database for Medicago truncatula
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DOI：
10.1093/bioinformatics/btm040
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发表时间：
2007-06-01
期刊：
影响因子：
5.8
通讯作者：
Sumner, Lloyd W.
中科院分区：
文献类型：
--
作者：
Urbanczyk-Wochniak, Ewa;Sumner, Lloyd W.
动机：必须需要整合功能基因组学数据，以获得对结果的更全面的系统生物学观点。我们认为，这是通过在代谢途径的生物学环境中可视化数据来实现的。因此，使用代谢途径重建来预测Medicago truncatula的代谢组成，并设计了这些途径以实现综合功能基因组学数据的相关可视化。回报：代谢途径重建用于生成用于M. truncatula（MediccyC）的途径数据库数据库（Mediccyc）的途径数据库（Mediccyc） ，目前具有250多个具有相关基因，酶和代谢产物的途径。 MediccyC是从225000 M以上的M. truncatula est（MTGI版本8.0）组装的，并使用途径工具软件和Metacyc数据库组装了可用的基因组序列。通过与其他植物数据库（如Aracyc和RiceCyc）进行比较，验证了MediccyC中预测的途径。与其他植物数据库的比较提供了有关酶仍缺少的酶的关键信息，但目前不完整的M. truncatula基因组测序项目。进一步手动策划了MediccyC，以去除非植物途径，并根据可用的文献和内部专业知识对包括异黄素，木质素和三萜皂苷生物合成在内的Medicago特异性途径进行了修改或添加。代谢分析实验中鉴定出的其他代谢产物也用于途径预测。一旦完成了代谢重建，MediccyC就会设计为在代谢途径的生物学环境中可视化截骨曲霉功能基因组学数据集。
Motivation: There is an imperative need to integrate functional genomics data to obtain a more comprehensive systems-biology view of the results. We believe that this is best achieved through the visualization of data within the biological context of metabolic pathways. Accordingly, metabolic pathway reconstruction was used to predict the metabolic composition for Medicago truncatula and these pathways were engineered to enable the correlated visualization of integrated functional genomics data.Results: Metabolic pathway reconstruction was used to generate a pathway database for M. truncatula (MedicCyc), which currently features more than 250 pathways with related genes, enzymes and metabolites. MedicCyc was assembled from more than 225000 M. truncatula ESTs (MtGI Release 8.0) and available genomic sequences using the Pathway Tools software and the MetaCyc database. The predicted pathways in MedicCyc were verified through comparison with other plant databases such as AraCyc and RiceCyc. The comparison with other plant databases provided crucial information concerning enzymes still missing from the ongoing, but currently incomplete M. truncatula genome sequencing project. MedicCyc was further manually curated to remove non-plant pathways, and Medicago-specific pathways including isoflavonoid, lignin and triterpene saponin biosynthesis were modified or added based upon available literature and in-house expertise. Additional metabolites identified in metabolic profiling experiments were also used for pathway predictions. Once the metabolic reconstruction was completed, MedicCyc was engineered to visualize M. truncatula functional genomics datasets within the biological context of metabolic pathways.