MetabNet: an R package for metabolic association analysis of high-resolution metabolomics data

被引：37

作者：

Uppal, Karan ^{[1
]}

Soltow, Quinlyn A. ^{[1
]}

Promislow, Daniel E. L. ^{[2
]}

Wachtman, Lynn M. ^{[3
]}

Quyyumi, Arshed Ali ^{[4
]}

Jones, Dean P. ^{[1
]}

机构：

[1] Emory Univ, Dept Med, Div Pulm Med, Atlanta, GA 30322 USA

[2] Univ Washington, Dept Pathol, Seattle, WA 98195 USA

[3] Harvard Univ, New England Reg Primate Res Ctr, Southborough, MA USA

[4] Emory Univ, Dept Med, Div Cardiol, Atlanta, GA 30322 USA

来源：

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY | 2015年 / 3卷

关键词：

metabolomics; metabolite identification; metabolic networks; metabolic pathways; targeted MWAS; choline;

D O I：

10.3389/fbioe.2015.00087

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Liquid-chromatography high-resolution mass spectrometry provides capability to measure >40,000 ions derived from metabolites in biologic samples. This presents challenges to confirm identities of known chemicals and delineate potential metabolic pathway associations of unidentified chemicals. We provide an R package for metabolic network analysis, MetabNet, to perform targeted metabolome-wide association study of specific metabolites to facilitate detection of their related metabolic pathways and network structures.

引用

页数：6

共 22 条

[1] AStream: an R package for annotating LC/MS metabolomic data
Alonso, Arnald
Julia, Antonio
Beltran, Antoni
Vinaixa, Maria
Diaz, Marta
Ibanez, Lourdes
Correig, Xavier
Marsal, Sara
[J]. BIOINFORMATICS, 2011, 27 (09) : 1339 - 1340
[2] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING
BENJAMINI, Y
HOCHBERG, Y
[J]. JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) : 289 - 300
[3] Untargeted Plasma Metabolite Profiling Reveals the Broad Systemic Consequences of Xanthine Oxidoreductase Inactivation in Mice
Chen, Qiuying
Park, Hyeong-Cheon
Goligorsky, Michael S.
Chander, Praveen
Fischer, Steven M.
Gross, Steven S.
[J]. PLOS ONE, 2012, 7 (06):
[4] Metabolome-wide association study of phenylalanine in plasma of common marmosets
Go, Young-Mi
Walker, Douglas I.
Soltow, Quinlyn A.
Uppal, Karan
Wachtman, Lynn M.
Strobel, Fredrick H.
Pennell, Kurt
Promislow, Daniel E. L.
Jones, Dean P.
[J]. AMINO ACIDS, 2015, 47 (03) : 589 - 601
[5] Toward 'Omic Scale Metabolite Profiling: A Dual Separation-Mass Spectrometry Approach for Coverage of Lipid and Central Carbon Metabolism
Ivanisevic, Julijana
Zhu, Zheng-Jiang
Plate, Lars
Tautenhahn, Ralf
Chen, Stephen
O'Brien, Peter J.
Johnson, Caroline H.
Marletta, Michael A.
Patti, Gary J.
Siuzdak, Gary
[J]. ANALYTICAL CHEMISTRY, 2013, 85 (14) : 6876 - 6884
[6] A practical approach to detect unique metabolic patterns for personalized medicine
Johnson, Jennifer M.
Yu, Tianwei
Strobel, Frederick H.
Jones, Dean P.
[J]. ANALYST, 2010, 135 (11) : 2864 - 2870
[7] Nutritional Metabolomics: Progress in Addressing Complexity in Diet and Health
Jones, Dean P.
Park, Youngja
Ziegler, Thomas R.
[J]. ANNUAL REVIEW OF NUTRITION, VOL 32, 2012, 32 : 183 - +
[8] The KEGG databases at GenomeNet
Kanehisa, M
Goto, S
Kawashima, S
Nakaya, A
[J]. NUCLEIC ACIDS RESEARCH, 2002, 30 (01) : 42 - 46
[9] Predicting Network Activity from High Throughput Metabolomics
Li, Shuzhao
Park, Youngja
Duraisingham, Sai
Strobel, Frederick H.
Khan, Nooruddin
Soltow, Quinlyn A.
Jones, Dean P.
Pulendran, Bali
[J]. PLOS COMPUTATIONAL BIOLOGY, 2013, 9 (07)
[10] Metabolite Identification for Mass Spectrometry-Based Metabolomics Using Multiple Types of Correlated Ion Information
Lynn, Ke-Shiuan
Cheng, Mei-Ling
Chen, Yet-Ran
Hsu, Chin
Chen, Ann
Lih, T. Mamie
Chang, Hui-Yin
Huang, Ching-jang
Shiao, Ming-Shi
Pan, Wen-Harn
Sung, Ting-Yi
Hsu, Wen-Lian
[J]. ANALYTICAL CHEMISTRY, 2015, 87 (04) : 2143 - 2151

← 1 2 3 →