MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity.
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity.
复制标题
DOI：
10.1186/1471-2105-13-99
复制
发表时间：
2012-05-16
影响因子：
3
通讯作者：
Fiehn O
中科院分区：
文献类型：
--
作者：
Barupal DK;Haldiya PK;Wohlgemuth G;Kind T;Kothari SL;Pinkerton KE;Fiehn O
暴露于环境烟草烟雾（ETS）导致儿童肺部疾病和感染的发病率较高。为了研究可能在肺部疾病之前发生的生化变化，将暴露于ETS的大鼠对胎儿和母体肺和血浆的代谢组学影响与过滤空气对照动物进行了比较。基因组重建的代谢途径可用于绘制和解释代谢网络中的失调。然而，基于质谱的非靶向代谢组学数据集通常包含许多尚未报道与酶促反应相关的代谢物。因此，依赖于当前生物化学数据库的网络可视化是不完整的，并且也无法可视化新的、结构上未识别的代谢物。我们提出了一种新的方法来整合生化途径和化学关系映射网络图（MetaMapp）中所有检测到的代谢物使用KEGG反应物对数据库，Tanimoto化学和NIST质谱相似性分数。在胎儿和母亲的肺，并在母体血浆从孕鼠暴露于环境烟草烟雾（ETS），459独特的代谢产物，包括179个结构鉴定的化合物，检测气相色谱飞行时间质谱（GC-TOF MS）和BinBase数据处理。Cytoscape中的MetaMapp图与传统的生化映射方法相比，显示出更清晰的代谢模块化和完整的内容可视化。使用这些图对差异统计结果进行Cytoscape可视化显示，总体而言，胎仔肺代谢比母鼠的肺和血液代谢受损更严重。与对照动物相比，暴露于ETS的母鼠的胎仔表达的脂质和核苷酸水平较低，能量代谢中间产物的量较高，表明细胞分裂代谢物、结构蛋白和对肺发育至关重要的脂质的生物合成速率较低。MetaMapp图表有效地将基于质谱的代谢组学数据集可视化为Cytoscape中的网络图，并突出显示可能与产前暴露于ETS的儿童的肺部疾病和感染率较高相关的代谢改变。MetaMapp脚本可以在http://metamapp.fiehnlab.ucdavis.edu上访问。
Exposure to environmental tobacco smoke (ETS) leads to higher rates of pulmonary diseases and infections in children. To study the biochemical changes that may precede lung diseases, metabolomic effects on fetal and maternal lungs and plasma from rats exposed to ETS were compared to filtered air control animals. Genome- reconstructed metabolic pathways may be used to map and interpret dysregulation in metabolic networks. However, mass spectrometry-based non-targeted metabolomics datasets often comprise many metabolites for which links to enzymatic reactions have not yet been reported. Hence, network visualizations that rely on current biochemical databases are incomplete and also fail to visualize novel, structurally unidentified metabolites. We present a novel approach to integrate biochemical pathway and chemical relationships to map all detected metabolites in network graphs (MetaMapp) using KEGG reactant pair database, Tanimoto chemical and NIST mass spectral similarity scores. In fetal and maternal lungs, and in maternal blood plasma from pregnant rats exposed to environmental tobacco smoke (ETS), 459 unique metabolites comprising 179 structurally identified compounds were detected by gas chromatography time of flight mass spectrometry (GC-TOF MS) and BinBase data processing. MetaMapp graphs in Cytoscape showed much clearer metabolic modularity and complete content visualization compared to conventional biochemical mapping approaches. Cytoscape visualization of differential statistics results using these graphs showed that overall, fetal lung metabolism was more impaired than lungs and blood metabolism in dams. Fetuses from ETS-exposed dams expressed lower lipid and nucleotide levels and higher amounts of energy metabolism intermediates than control animals, indicating lower biosynthetic rates of metabolites for cell division, structural proteins and lipids that are critical for in lung development. MetaMapp graphs efficiently visualizes mass spectrometry based metabolomics datasets as network graphs in Cytoscape, and highlights metabolic alterations that can be associated with higher rate of pulmonary diseases and infections in children prenatally exposed to ETS. The MetaMapp scripts can be accessed at http://metamapp.fiehnlab.ucdavis.edu.