An Enrichment Method for Obtaining Biologically Significant Genes from Statistically Significant Differentially Expressed Genes in Comparative Transcriptomics

TL;DR

This paper introduces an enrichment method to identify biologically significant genes from differentially expressed genes, addressing challenges posed by drastic transcriptome changes due to environmental factors like drug concentrations.

Contribution

The study proposes a novel enrichment technique to better extract biologically relevant genes from differential expression data in comparative transcriptomics.

Findings

Enrichment method improves detection of significant genes

High drug concentrations cause drastic transcriptome shifts

Method aids in identifying biologically meaningful genes

Abstract

Cells coordinate adjustments in genome expression to accommodate changes in their environment. A drug in culture media for in vitro preclinical testing sometimes cause drastic regime shifting of genome expression system depending on the concentrations; e.g. primary cultured cells exposed to high concentrations of phenobarbital (>0.25 mM) recovered their tissue-specific character as part of an individual organism. Drastic changes of transcriptomes interrupt discovering biologically significant genes in comparative transcriptomics. Here, we compared the amount of environmental changes and the amount of transcriptome changes using phenobarbital and the Chinese hamster ovary derived established continuous cell line CHO-K1; immortalized cell lines are accepted for in vitro preclinical testing then primary cultured cells.