Method, program product and apparatus for discovering functionally similar gene expression profiles

摘要

Genes to be compared are listed by their gene expression profiles and processed with a similar sequences algorithm that is a time and intensity invariant correlation function to obtain a data set of gene expression pairs and a match fraction for each pair. A threshold match fraction is chosen and a null set is created to hold indices of genes accounted for. Genes are then assigned to clusters by match fraction value if they have a match fraction greater than the threshold. Genes are then removed from clusters if they are represented in more than one cluster by removing a first gene from a cluster when another cluster has another gene with a higher match fraction with the first gene. When the difference between maximum match fraction values for pairs including a first gene in a first cluster and the first gene a second cluster is small, the first gene may be removed from the first cluster even when another gene in the first cluster has a higher match fraction with the first gene than the first gene has with a third gene in a second cluster. This occurs when the number of similar subsequences for the pair including the first gene in the first cluster is higher than the number of similar subsequences for the pair including the first gene in the second cluster.