دورية أكاديمية
Omics Untargeted Key Script : R-Based Software Toolbox for Untargeted Metabolomics with Bladder Cancer Biomarkers Discovery Case Study.
| العنوان: | Omics Untargeted Key Script : R-Based Software Toolbox for Untargeted Metabolomics with Bladder Cancer Biomarkers Discovery Case Study. |
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| المؤلفون: | Plyushchenko IV; Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia., Fedorova ES; A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071 Moscow, Russia., Potoldykova NV; Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, 119992 Moscow, Russia., Polyakovskiy KA; Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, 119992 Moscow, Russia., Glukhov AI; Biology Department, Lomonosov Moscow State University, 119991 Moscow, Russia.; Department of Biochemistry, Sechenov First Moscow State Medical University, 119991 Moscow, Russia., Rodin IA; Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia.; Department of Epidemiology and Evidence-Based Medicine, Sechenov First Moscow State Medical University, 119435 Moscow, Russia. |
| المصدر: | Journal of proteome research [J Proteome Res] 2022 Mar 04; Vol. 21 (3), pp. 833-847. Date of Electronic Publication: 2021 Jun 23. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Washington, D.C. : American Chemical Society, c2002- |
| مواضيع طبية MeSH: | Neoplasms* , Urinary Bladder*, Biomarkers ; Biomarkers, Tumor ; Humans ; Metabolomics/methods ; Software |
| مستخلص: | Large-scale untargeted LC-MS-based metabolomic profiling is a valuable source for systems biology and biomarker discovery. Data analysis and processing are major tasks due to the high complexity of generated signals and the presence of unwanted variations. In the present study, we introduce an R-based open-source collection of scripts called OUKS ( Omics Untargeted Key Script ), which provides comprehensive data processing. OUKS is developed by integrating various R packages and metabolomics software tools and can be easily set up and prepared to create a custom pipeline. Novel computational features are related to quality control samples-based signal processing and are implemented by gradient boosting, tree-based, and other nonlinear regression algorithms. Bladder cancer biomarkers discovery study which is based on untargeted LC-MS profiling of urine samples is performed to demonstrate exhaustive functionality of the developed software tool. Unique examination among dozens of metabolomics-specific data curation methods was carried out at each processing step. As a result, potential biomarkers were identified, statistically validated, and described by metabolism disorders. Our study demonstrates that OUKS helps to make untargeted LC-MS metabolomic profiling with the latest computational features readily accessible in a ready-to-use unified manner to a research community. |
| فهرسة مساهمة: | Keywords: R programming; bladder cancer; data analysis; metabolomics; untargeted profiling |
| المشرفين على المادة: | 0 (Biomarkers) 0 (Biomarkers, Tumor) |
| تواريخ الأحداث: | Date Created: 20210623 Date Completed: 20220419 Latest Revision: 20220419 |
| رمز التحديث: | 20221213 |
| DOI: | 10.1021/acs.jproteome.1c00392 |
| PMID: | 34161108 |
| قاعدة البيانات: | MEDLINE |
Find this issue from the American Chemical Society | تدمد: | 1535-3907 |
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| DOI: | 10.1021/acs.jproteome.1c00392 |