metabolomics_data_using_OPLS-DA

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SIMCA Tutorial Analysing NMR Metabolomics data using OPLS-DA •

••

• 1

Analysing NMR Metabolomics data using

OPLS-DA

Background

A gene encoding MYB transcription factor, with unknown function, PttMYB76, was selected from a

library of poplar trees for metabolomic characterization of the growth process in Poplar trees.

Objective

The objective of this exercise is to shed some light on how PCA and OPLS-DA may be used in state-of-

the-art Metabolomics. In particular, the objectives are to:

• Demonstrate how to analyze metabolomics data from two sets of samples representing one

control group and one treated group

o Using PCA to review data, identify patterns and trends

• Demonstrate how to identify differences and putative biomarkers in different sample groups and

compare the strength of OPLS-DA compared to PCA

o Using OPLS-DA

• Describe the model diagnostics of an OPLS-DA model

Data

In total, the data set contains N = 57 observations, 6 trees divided into segments of 8 by the internode of

the tree plus analytical replicates and K = 655 variables (

H-NMR chemical shift regions bucket with

0.02ppm). The internode represents the growth direction of a plant. Internode 1 is the top of the plant and

8 is the bottom. The observations (trees) are divided in two groups (“classes”):

• MYB76 poplar plant (Ai, Bi, Ci)- Class 2

• Wild type Poplar plant (Di, Ei, Fi)- Class 1

The name settings A, B, C corresponds to MYB76 plants and D, E, F to the wild type (control) plants.

The i after the letter corresponds to the internode number of the plant. The last 12 experiments in the

dataset are analytical replicates i.e. samples that were run twice in the spectrometer. The analytical

replicates are marked with r1 or r2 after the internode number.

The plant material was analyzed by a 500 MHz NMR spectrometer equipped with a HR/MAS probe. The

H NMR spectra were reduced by binning all of the data points over a 0.02 ppm region. Data points

between 4.2- 5.6 ppm, corresponding to water resonances, were excluded, leaving a total of 655 NMR

spectral regions as variables for the multivariate modelling. A more detailed description of the

experimental conditions is found in [

S. Wiklund et.al A new metabonomic strategy for analysing the growth process of the poplar tree. Plant Biotechnology Journal 2005 3 pp 353-362

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