Dynamic range-based distance measure for microarray expressions and a fast gene-ordering algorithm.
This investigation deals with a new distance measure for genes using their microarray expressions and a new algorithm for fast gene ordering without clustering. This distance measure is called "Maxrange distance," where the distance between two genes corresponding to a particular type of experiment is computed using a normalization factor, which is dependent on the dynamic range of the gene expression values of that experiment. The new gene-ordering method called "Minimal Neighbor" is based on the concept of nearest neighbor heuristic involving O(n2) time complexity. The superiority of this distance measure and the comparability of the ordering algorithm have been extensively established on widely studied microarray data sets by performing statistical tests. An interesting application of this ordering algorithm is also demonstrated for finding useful groups of genes within clusters obtained from a nonhierarchical clustering method like the self-organizing map.
Ray
Shubhra Sankar
SS
Bandyopadhyay
Sanghamitra
S
Pal
Sankar K
SK
D000465:Algorithms; D001185:Artificial Intelligence; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D008957:Models, Genetic; D005810:Multigene Family / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*