A novel approach for the analysis of time-course gene expression data based on computing with words

[Display omitted] •Analysis of time-course gene expression data based on Zadeh’s Computing with Words.•A new time-series pattern mining technique for dynamical analysis of gene expression.•Pattern discovery in terms of both linguistic and type-2 fuzzy-logic descriptions.•Case study: Analysis of transcriptional response of cancer cells to anticancer drugs.•FuzzGene: An open-source software package for implementation of the proposed method. In this paper, a novel approach is proposed for the analysis of time-course gene expression data based on the path-breaking work of Zadeh, Computing with Words. This method can automatically discover the patterns of temporal gene expression profile in terms of two distinguishing descriptions: linguistic description that is understandable and interpretable for human inference; and type-2 fuzzy description that is suitable for robust machine inference in the presence of uncertainty. In contrast to conventional static data mining methods which focus on the steady-state gene expression levels, the proposed scheme is a new time-series pattern mining technique for dynamical modeling of gene expression. To evaluate the performance of this paradigm, it is applied to a case study dataset from Gene Expression Omnibus (GEO) which includes the temporal transcriptional profile of human colon cancer cells. The goal is to investigate the pharmacodynamics of two anticancer drugs. The transient and steady-state analysis of the transcriptional response clearly demonstrates the ability of the proposed approach to reveal the pharmacodynamical effects of drug type and dosage on the expression of genes.