Literature DB >> 20233650

Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology.

Wenjiang J Fu1, Arnold J Stromberg, Kert Viele, Raymond J Carroll, Guoyao Wu.   

Abstract

Over the past 2 decades, there have been revolutionary developments in life science technologies characterized by high throughput, high efficiency, and rapid computation. Nutritionists now have the advanced methodologies for the analysis of DNA, RNA, protein, low-molecular-weight metabolites, as well as access to bioinformatics databases. Statistics, which can be defined as the process of making scientific inferences from data that contain variability, has historically played an integral role in advancing nutritional sciences. Currently, in the era of systems biology, statistics has become an increasingly important tool to quantitatively analyze information about biological macromolecules. This article describes general terms used in statistical analysis of large, complex experimental data. These terms include experimental design, power analysis, sample size calculation, and experimental errors (Type I and II errors) for nutritional studies at population, tissue, cellular, and molecular levels. In addition, we highlighted various sources of experimental variations in studies involving microarray gene expression, real-time polymerase chain reaction, proteomics, and other bioinformatics technologies. Moreover, we provided guidelines for nutritionists and other biomedical scientists to plan and conduct studies and to analyze the complex data. Appropriate statistical analyses are expected to make an important contribution to solving major nutrition-associated problems in humans and animals (including obesity, diabetes, cardiovascular disease, cancer, ageing, and intrauterine growth retardation). (c) 2010 Elsevier Inc. All rights reserved.

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Year:  2010        PMID: 20233650      PMCID: PMC2885517          DOI: 10.1016/j.jnutbio.2009.11.007

Source DB:  PubMed          Journal:  J Nutr Biochem        ISSN: 0955-2863            Impact factor:   6.048


  81 in total

1.  Assessing gene significance from cDNA microarray expression data via mixed models.

Authors:  R D Wolfinger; G Gibson; E D Wolfinger; L Bennett; H Hamadeh; P Bushel; C Afshari; R S Paules
Journal:  J Comput Biol       Date:  2001       Impact factor: 1.479

Review 2.  Statistical design and the analysis of gene expression microarray data.

Authors:  M K Kerr; G A Churchill
Journal:  Genet Res       Date:  2001-04       Impact factor: 1.588

3.  Power and sample size for DNA microarray studies.

Authors:  Mei-Ling Ting Lee; G A Whitmore
Journal:  Stat Med       Date:  2002-12-15       Impact factor: 2.373

4.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Authors:  Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Journal:  Anal Chem       Date:  2002-10-15       Impact factor: 6.986

5.  A correlation algorithm for the automated quantitative analysis of shotgun proteomics data.

Authors:  Michael J MacCoss; Christine C Wu; Hongbin Liu; Rovshan Sadygov; John R Yates
Journal:  Anal Chem       Date:  2003-12-15       Impact factor: 6.986

6.  Sample size determination in microarray experiments for class comparison and prognostic classification.

Authors:  Kevin Dobbin; Richard Simon
Journal:  Biostatistics       Date:  2005-01       Impact factor: 5.899

7.  PepNovo: de novo peptide sequencing via probabilistic network modeling.

Authors:  Ari Frank; Pavel Pevzner
Journal:  Anal Chem       Date:  2005-02-15       Impact factor: 6.986

Review 8.  Environmental toxicity, nutrition, and gene interactions in the development of atherosclerosis.

Authors:  Bernhard Hennig; Elizabeth Oesterling; Michal Toborek
Journal:  Nutr Metab Cardiovasc Dis       Date:  2006-03-31       Impact factor: 4.222

9.  A physical map of the human genome.

Authors:  J D McPherson; M Marra; L Hillier; R H Waterston; A Chinwalla; J Wallis; M Sekhon; K Wylie; E R Mardis; R K Wilson; R Fulton; T A Kucaba; C Wagner-McPherson; W B Barbazuk; S G Gregory; S J Humphray; L French; R S Evans; G Bethel; A Whittaker; J L Holden; O T McCann; A Dunham; C Soderlund; C E Scott; D R Bentley; G Schuler; H C Chen; W Jang; E D Green; J R Idol; V V Maduro; K T Montgomery; E Lee; A Miller; S Emerling; R Gibbs; S Scherer; J H Gorrell; E Sodergren; K Clerc-Blankenburg; P Tabor; S Naylor; D Garcia; P J de Jong; J J Catanese; N Nowak; K Osoegawa; S Qin; L Rowen; A Madan; M Dors; L Hood; B Trask; C Friedman; H Massa; V G Cheung; I R Kirsch; T Reid; R Yonescu; J Weissenbach; T Bruls; R Heilig; E Branscomb; A Olsen; N Doggett; J F Cheng; T Hawkins; R M Myers; J Shang; L Ramirez; J Schmutz; O Velasquez; K Dixon; N E Stone; D R Cox; D Haussler; W J Kent; T Furey; S Rogic; S Kennedy; S Jones; A Rosenthal; G Wen; M Schilhabel; G Gloeckner; G Nyakatura; R Siebert; B Schlegelberger; J Korenberg; X N Chen; A Fujiyama; M Hattori; A Toyoda; T Yada; H S Park; Y Sakaki; N Shimizu; S Asakawa; K Kawasaki; T Sasaki; A Shintani; A Shimizu; K Shibuya; J Kudoh; S Minoshima; J Ramser; P Seranski; C Hoff; A Poustka; R Reinhardt; H Lehrach
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

Review 10.  Mechanisms of colorectal and lung cancer prevention by vegetables: a genomic approach.

Authors:  Simone G J van Breda; Theo M C M de Kok; Joost H M van Delft
Journal:  J Nutr Biochem       Date:  2007-07-24       Impact factor: 6.048

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  26 in total

Review 1.  Expanding the frontiers of population nutrition research: new questions, new methods, and new approaches.

Authors:  David L Pelletier; Christine M Porter; Gregory A Aarons; Sara E Wuehler; Lynnette M Neufeld
Journal:  Adv Nutr       Date:  2013-01-01       Impact factor: 8.701

2.  Metabolomic analysis of amino acid and energy metabolism in rats supplemented with chlorogenic acid.

Authors:  Zheng Ruan; Yuhui Yang; Yan Zhou; Yanmei Wen; Sheng Ding; Gang Liu; Xin Wu; Peng Liao; Zeyuan Deng; Houssein Assaad; Guoyao Wu; Yulong Yin
Journal:  Amino Acids       Date:  2014-06-14       Impact factor: 3.520

3.  Comparisons of treatment means when factors do not interact in two-factorial studies.

Authors:  Jiawei Wei; Raymond J Carroll; Kathryn K Harden; Guoyao Wu
Journal:  Amino Acids       Date:  2011-05-06       Impact factor: 3.520

Review 4.  Proline and hydroxyproline metabolism: implications for animal and human nutrition.

Authors:  Guoyao Wu; Fuller W Bazer; Robert C Burghardt; Gregory A Johnson; Sung Woo Kim; Darrell A Knabe; Peng Li; Xilong Li; Jason R McKnight; M Carey Satterfield; Thomas E Spencer
Journal:  Amino Acids       Date:  2010-08-10       Impact factor: 3.520

5.  Dietary supplementation with L-arginine between days 14 and 25 of gestation enhances NO and polyamine syntheses and the expression of angiogenic proteins in porcine placentae.

Authors:  Mohammed A Elmetwally; Xilong Li; Gregory A Johnson; Robert C Burghardt; Cassandra M Herring; Avery C Kramer; Cynthia J Meininger; Fuller W Bazer; Guoyao Wu
Journal:  Amino Acids       Date:  2021-11-06       Impact factor: 3.520

6.  Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life.

Authors:  Jim Kaput; Ben van Ommen; Bas Kremer; Corrado Priami; Jacqueline Pontes Monteiro; Melissa Morine; Fre Pepping; Zoey Diaz; Michael Fenech; Yiwu He; Ruud Albers; Christian A Drevon; Chris T Evelo; Robert E W Hancock; Carel Ijsselmuiden; L H Lumey; Anne-Marie Minihane; Michael Muller; Chiara Murgia; Marijana Radonjic; Bruno Sobral; Keith P West
Journal:  Genes Nutr       Date:  2013-12-22       Impact factor: 5.523

Review 7.  Data analysis methods for defining biomarkers from omics data.

Authors:  Chao Li; Zhenbo Gao; Benzhe Su; Guowang Xu; Xiaohui Lin
Journal:  Anal Bioanal Chem       Date:  2021-12-24       Impact factor: 4.142

8.  Epigenetic influences in the aetiology of cancers arising from breast and prostate: a hypothesised transgenerational evolution in chromatin accessibility.

Authors:  Francis L Martin
Journal:  ISRN Oncol       Date:  2013-02-03

Review 9.  Analysis of energy expenditure in diet-induced obese rats.

Authors:  Houssein Assaad; Kang Yao; Carmen D Tekwe; Shuo Feng; Fuller W Bazer; Lan Zhou; Raymond J Carroll; Cynthia J Meininger; Guoyao Wu
Journal:  Front Biosci (Landmark Ed)       Date:  2014-06-01

10.  Associations between dietary patterns and gene expression profiles of healthy men and women: a cross-sectional study.

Authors:  Annie Bouchard-Mercier; Ann-Marie Paradis; Iwona Rudkowska; Simone Lemieux; Patrick Couture; Marie-Claude Vohl
Journal:  Nutr J       Date:  2013-02-12       Impact factor: 3.271

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