Adaptation of E.coli and Alternating Substrate Conditions

Karabekmez M. E.

2nd International Conference on Life and Engineering Sciences, İstanbul, Turkey, 27 - 29 June 2019, pp.1

  • Publication Type: Conference Paper / Summary Text
  • City: İstanbul
  • Country: Turkey
  • Page Numbers: pp.1


                                                                                                                                                    Adaptation of E.coli to Alternating Substrate Conditions


Muhammed Erkan KARABEKMEZ1

1Department of Bioengineering, Faculty of Engineering and Natural Sciences,

Istanbul Medeniyet University, Istanbul-TURKEY


The expression of genes that are functionally related is considered to change together in response 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 prefered 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.


Key words: WGCNA, Transcriptomics, Asymmetric Sigmoid Function.