Gene Updater: a web tool that autocorrects and updates for Excel misidentified gene names

Abstract

Opening and processing gene expression data files in Excel runs into the inadvertent risk of converting gene names to dates. As pathway analysis tools rely on gene symbols to query against pathway databases, the genes that are converted to dates will not be recognized, potentially causing voids in pathway analysis. Molecular pathways related to cell division, exocytosis, cilium assembly, protein ubiquitination and nitric oxide biosynthesis were found to be most affected by Excel auto-conversion. A plausible solution is hence to update these genes and dates to the newly approved gene names as recommended by the HUGO Gene Nomenclature Committee (HGNC), which are resilient to Excel auto-conversion. Herein, we developed a web tool with Streamlit that can convert old gene names and dates back into the new gene names recommended by HGNC. The web app is named Gene Updater, which is open source and can be either hosted locally or at https://share.streamlit.io/kuanrongchan/date-to-gene-converter/main/date_gene_tool.py. Additionally, as Mar-01 and Mar-02 can each be potentially mapped to 2 different gene names, users can assign the date terms to the appropriate gene names within the Gene Updater web tool. This user-friendly web tool ensures that the accuracy and integrity of gene expression data is preserved by minimizing errors in labelling gene names due to Excel auto-conversions.