Innovative GenExpA software for selecting suitable reference genes for reliable normalization of gene expression in melanoma

Abstract

Melanoma is characterized by a high mutation rate and the proper reference selection is a serious problem. The algorithms commonly used to select the best stable reference gene or pair of genes in RT-qPCR data analysis have their limitations which affects the interpretation of the results and drawing conclusions. For reliable assessment of the B4GALT genes expression changes in melanoma and comparing them to their expression levels in melanocytes, we implemented an innovative GenExpA software. We proposed selection of the best reference by combining the NormFinder algorithm with progressive removal of the least stable gene from the candidate genes in a given experimental model and the set of daughter models assigned to it. The reliability of references is validated by normalizing of target gene expression level through all models and is described by the coherence score. The software performs statistical analyses and generates results in the form of ready-to-use graphs and tables. GenExpA is a promising tool for basic research; it produces analyses of target gene expression in a manner independent of the experimental model and the normalizer. GenExpA and its manual is freely available at https://drive.google.com/drive/folders/1FcpBtEc_bKPvEnM5GcPZerBb_Tw_fCkt?usp=sharing or https://www.sciencemarket.pl/baza-programow-open-source#oferty. Supplemental materials are deposited under DOI number: 10.5281/zenodo.4544296.