A multiway approach to data integration in systems biology based on Tucker3 and N-PLS

被引：25

作者：

Conesa, Ana ^{[1
]}

Prats-Montalban, Jose M. ^{[2
]}

Tarazona, Sonia ^{[1
,2
]}

Jose Nueda, Ma ^{[3
]}

Ferrer, Alberto ^{[2
]}

机构：

[1] Ctr Invest Principe Felipe, Bioinformat & Genom Dept, Valencia, Spain

[2] Univ Politecn Valencia, Dept Estadist & Invest Operat Aplicadas & Calidad, Valencia, Spain

[3] Univ Alicante, Dept Estadist & Invest Operat, Alicante, Spain

来源：

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS | 2010年 / 104卷 / 01期

关键词：

Multi-way analysis; N-PLS; Tucker3; Data integration; Omics data; Systems biology; PRINCIPAL COMPONENT ANALYSIS; GENE-EXPRESSION; TRANSCRIPT; METABOLOMICS; BIOSYNTHESIS; PROFILES; NETWORKS; ASCA; TOOL;

D O I：

10.1016/j.chemolab.2010.06.004

中图分类号：

TP [自动化技术、计算机技术];

学科分类号：

0812 ;

摘要：

This paper discusses the potential of multi-way projection methods for analysing multifactorial data structures to identify underlying components of variability that interconnect different blocks of omics variables. We explore their suitability for explorative and variable selection analysis of systems biology data where different types of biological parameters are studied together. These methodologies were applied to the integrative analysis of a functional genomics dataset where transcriptomics, metabolomics and physiological data are available. Our results show that multiway methods are suited to accommodate multifactorial omics experiments and to analyse relationships between different biochemical layers. Additionally, strategies are presented for variable selection in the context of omics data and for interpreting results at the level of cellular pathways. (C) 2010 Elsevier B.V. All rights reserved.

引用

页码：101 / 111

页数：11

共 42 条

[1] FatiGO:: a web tool for finding significant associations of Gene Ontology terms with groups of genes [J].

Al-Shahrour, F ;

Díaz-Uriarte, R ;

Dopazo, J .

BIOINFORMATICS, 2004, 20 (04) :578-580

[2] From genes to functional classes in the study of biological systems [J].

Al-Shahrour, Fatima ;

Arbiza, Leonardo ;

Dopazo, Hernan ;

Huerta-Cepas, Jaime ;

Minguez, Pablo ;

Montaner, David ;

Dopazo, Joaquin .

BMC BIOINFORMATICS, 2007, 8 (1)

[3] PARAFAC. Tutorial and applications [J].

Bro, R .

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 1997, 38 (02) :149-171

[4] Centering and scaling in component analysis [J].

Bro, R ;

Smilde, AK .

JOURNAL OF CHEMOMETRICS, 2003, 17 (01) :16-33

[5] Exploring complex interactions in designed data using GEMANOVA. Color changes in fresh beef during storage [J].

Bro, R ;

Jakobsen, M .

JOURNAL OF CHEMOMETRICS, 2002, 16 (06) :294-304

[6] On the difference between low-rank and subspace approximation: improved model for multi-linear PLS regression [J].

Bro, R ;

Smilde, AK ;

de Jong, S .

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 2001, 58 (01) :3-13

[7]

Bro R, 1996, J CHEMOMETR, V10, P47, DOI 10.1002/(SICI)1099-128X(199601)10:1<47::AID-CEM400>3.0.CO

[8]

2-C

[9] Review on multiway analysis in chemistry - 2000-2005 [J].

Bro, Rasmus .

CRITICAL REVIEWS IN ANALYTICAL CHEMISTRY, 2006, 36 (3-4) :279-293

[10] Data integration in plant biology:: the O2PLS method for combined modeling of transcript and metabolite data [J].

Bylesjo, Max ;

Eriksson, Daniel ;

Kusano, Miyako ;

Moritz, Thomas ;

Trygg, Johan .

PLANT JOURNAL, 2007, 52 (06) :1181-1191

← 1 2 3 4 5 →