Correspondence analysis of microarray time-course data in case-control design.
Although different statistical approaches have been proposed for analyzing microarray time-course data, method for analyzing such data collected using the popular case-control design in clinical investigations has not been proposed perhaps due to the increased complexity for the existing parametric or non-parametric approaches. In this paper, we introduce a new multivariate data analyzing technique, the correspondence analysis, to analyze the high dimensional microarray time-course data in case-control design. We show, through an example on type 2 diabetes, how the nice features of the correspondence analysis can be use to explore the various time-course gene expression profiles that exist in the data. By coordinating and examining the projections on the reduced dimensions by both the genes and the time-course experiments, we are able to identify important genes and time-course patterns and make inferences on their biological relevance. Using the sample replicates, we propose a bootstrap procedure for inferring the significance of contributions on the leading dimensions by both the time-course experiments and the genes. Striking differences in the time-course patterns in the normal controls and diabetes patients have been revealed. In addition, the method also identifies genes that display similar or comparable time-course expression patterns shared by both the cases and the controls. We conclude that our correspondence analysis based approach can be a useful tool for analyzing high dimensional microarray data collected in clinical investigations.
Tan
Qihua
Q
Odense University Hospital, Odense, Denmark. qihua.tan@ouh.fyns-amt.dk
Brusgaard
Klaus
K
Kruse
Torben A
TA
Oakeley
Edward
E
Hemmings
Brian
B
Beck-Nielsen
Henning
H
Hansen
Lars
L
Gaster
Michael
M
D000465:Algorithms; D016022:Case-Control Studies; D003196:Computer Graphics; D003924:Diabetes Mellitus, Type 2 / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism*; D018450:Disease Progression; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D013223:Statistics as Topic; D013997:Time Factors; D014584:User-Computer Interface