Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.
Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.
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DOI：
10.1021/ac500734c
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发表时间：
2014-07-15
影响因子：
7.4
通讯作者：
Siuzdak, Gary
中科院分区：
文献类型：
--
作者：
Gowda, Harsha;Ivanisevic, Julijana;Johnson, Caroline H.;Kurczy, Michael E.;Benton, H. Paul;Rinehart, Duane;Thomas Nguyen;Ray, Jayashree;Kuehl, Jennifer;Arevalo, Bernardo;Westenskow, Peter D.;Wang, Junhua;Arkin, Adam P.;Deutschbauer, Adam M.;Patti, Gary J.;Siuzdak, Gary
XCMS Online（）是一个基于云的信息平台，旨在处理和可视化基于质谱的非靶向代谢组学数据。最初，该平台是为了两组比较而开发的，以匹配独立的“对照”与“疾病”实验设计。在这里，我们介绍了一个增强的XCMS在线界面，使用户能够执行依赖（配对）两组比较，荟萃分析和多组比较，全面的统计输出和交互式可视化工具。新纳入的统计检验涵盖了广泛的单变量分析。多组比较允许在多个类别的数据中识别差异表达的代谢物特征，而高阶荟萃分析有助于在多个两组比较中识别共享的代谢模式。考虑到这些数据集的复杂性，我们开发了一个交互式平台，用户可以通过调整各种参数的阈值和范围来真实的监控单变量（云图）和多变量（PCA图）数据分析的统计输出。在交互式云图上，代谢物特征可以通过其显著性水平（p值）、倍数变化、质荷比、保留时间和强度过滤掉。每个特征的变化模式可以在提取的离子色谱图和箱形图上可视化。交互式主成分分析包括分数、载荷和scree图，可以根据缩放标准进行调整。通过细菌应激反应的代谢组学分析和淋巴母细胞白血病细胞系的比较，证明了XCMS功能的实用性。
XCMS Online () is a cloud-based informatic platform designed to process and visualize mass-spectrometry-based, untargeted metabolomic data. Initially, the platform was developed for two-group comparisons to match the independent, “control” versus “disease” experimental design. Here, we introduce an enhanced XCMS Online interface that enables users to perform dependent (paired) two-group comparisons, meta-analysis, and multigroup comparisons, with comprehensive statistical output and interactive visualization tools. Newly incorporated statistical tests cover a wide array of univariate analyses. Multigroup comparison allows for the identification of differentially expressed metabolite features across multiple classes of data while higher order meta-analysis facilitates the identification of shared metabolic patterns across multiple two-group comparisons. Given the complexity of these data sets, we have developed an interactive platform where users can monitor the statistical output of univariate (cloud plots) and multivariate (PCA plots) data analysis in real time by adjusting the threshold and range of various parameters. On the interactive cloud plot, metabolite features can be filtered out by their significance level (p-value), fold change, mass-to-charge ratio, retention time, and intensity. The variation pattern of each feature can be visualized on both extracted-ion chromatograms and box plots. The interactive principal component analysis includes scores, loadings, and scree plots that can be adjusted depending on scaling criteria. The utility of XCMS functionalities is demonstrated through the metabolomic analysis of bacterial stress response and the comparison of lymphoblastic leukemia cell lines.
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影响因子：
30.8
作者：
Chung, Charles C.;Kanetsky, Peter A.;Wang, Zhaoming;Hildebrandt, Michelle A. T.;Koster, Roelof;Skotheim, Rolf I.;Kratz, Christian P.;Turnbull, Clare;Cortessis, Victoria K.;Bakken, Anne C.;Bishop, D. Timothy;Cook, Michael B.;Erickson, R. Loren;Fossa, Sophie D.;Jacobs, Kevin B.;Korde, Larissa A.;Kraggerud, Sigrid M.;Lothe, Ragnhild A.;Loud, Jennifer T.;Rahman, Nazneen;Skinner, Eila C.;Thomas, Duncan C.;Wu, Xifeng;Yeager, Meredith;Schumacher, Fredrick R.;Greene, Mark H.;Schwartz, Stephen M.;McGlynn, Katherine A.;Chanock, Stephen J.;Nathanson, Katherine L.
通讯作者：
Nathanson, Katherine L.
影响因子：
30.8
作者：
Barrett, Jeffrey C.;Clayton, David G.;Concannon, Patrick;Akolkar, Beena;Cooper, Jason D.;Erlich, Henry A.;Julier, Cecile;Morahan, Grant;Nerup, Jorn;Nierras, Concepcion;Plagnol, Vincent;Pociot, Flemming;Schuilenburg, Helen;Smyth, Deborah J.;Stevens, Helen;Todd, John A.;Walker, Neil M.;Rich, Stephen S.
通讯作者：
Rich, Stephen S.
影响因子：
3.6
作者：
Patti, Gary J.;Tautenhahn, Ralf;Johannsen, Darcy;Kalisiak, Ewa;Ravussin, Eric;Bruening, Jens C.;Dillin, Andrew;Siuzdak, Gary
通讯作者：
Siuzdak, Gary
影响因子：
7.4
作者：
Melamud E;Vastag L;Rabinowitz JD
通讯作者：
Rabinowitz JD
影响因子：
--
作者：
Kastenmueller, Gabi;Roemisch-Margl, Werner;Suhre, Karsten
通讯作者：
Suhre, Karsten