Using formal concept analysis for microarray data comparison.
Microarray technologies, which can measure tens of thousands of gene expression values simultaneously in a single experiment, have become a common research method for biomedical researchers. Computational tools to analyze microarray data for biological discovery are needed. In this paper, we investigate the feasibility of using formal concept analysis (FCA) as a tool for microarray data analysis. The method of FCA builds a (concept) lattice from the experimental data together with additional biological information. For microarray data, each vertex of the lattice corresponds to a subset of genes that are grouped together according to their expression values and some biological information related to gene function. The lattice structure of these gene sets might reflect biological relationships in the dataset. Similarities and differences between experiments can then be investigated by comparing their corresponding lattices according to various graph measures. We apply our method to microarray data derived from influenza-infected mouse lung tissue and healthy controls. Our preliminary results show the promise of our method as a tool for microarray data analysis.
Choi
V
V
Department of Computer Science, Virginia Tech, 660 McBryde Hall, Blacksburg, VA 24061, USA. vchoi@cs.vt.edu
Huang
Y
Y
Lam
V
V
Potter
D
D
Laubenbacher
R
R
Duca
K
K
D000465:Algorithms; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D005810:Multigene Family / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D025341:Principal Component Analysis