The Expression Ratio (HN-ratio) of Gene Expression Under Heat-stress and Non-stress Conditions in Human and Mouse.

After quantifying expression using the analysis pipeline ikra (https://github.com/yyoshiaki/ikra), expression ratios (HN-ratios) were calculated for data collected in pairs of HS and non-treatment conditions. The HN-ratios calculated for all genes were then classified as "upregulated," "downregulated," or "unchanged" if neither threshold was met, according to a defined threshold (5-fold or 1/5-fold in this study). This classification facilitates the interpretation of complicated gene expression data.

Gene expression data retrieval, processing, and quantification were performed using ikra (ver. 2.0.1), an automated human and mouse RNA-seq data analysis pipeline. Ikra is a tool that can automatically perform all the following processes: retrieval of FASTQ format files using the fasterq-dump program in the NCBI SRA tool kit (ver. 3.0.0), read quality control, and adapter trimming using Trim_galore (ver. 0.6.6) and transcript quantification using Salmon (ver. 1.9.0). The reference sequence sets of human GENCODE Release 37 (GRCh38.p13) and mouse GENCODE Release 26 (GRCm39) were used.

HN-ratio was calculated using codes used in previous papers (https://github.com/no85j/hypoxia_code).