A modified Soft-thresholding Approach in the Transcriptomic Analysis of Adaptation of E.coli to Alternating Substrate Conditions

Abstract

The expression of genes that are functionally related is considered to change together inresponse to deterioration of internal or external order. The system-level analysis of these changes has become widespread in recent years. Weighted gene co-expression network analysis (WGCNA) is an important tool in the literature. This method has two options in the form of hard and soft thresholding. The power function is used commonly in soft thresholding option. The other alternative of soft thresholding, symmetric sigmoid function, may give less importance to the meaningful co-expression data and not preferred frequently. Both functions has some drawbacks. In this study, it was tried to increase the efficiency of WGCNA approach by using asymmetric sigmoid function. RNA-seq dataset on adaptation of E.coli to alternating substrate conditions was re-investigated with this modified approach and its use was proven by GO and pathway enrichment analysis.