Computational Approach to Identifying Universal Macrophage Biomarkers

• Published in: Frontiers in physiology Vol. 11; p. 275
• Main Authors: Dang, Dharanidhar, Taheri, Sahar, Das, Soumita, Ghosh, Pradipta, Prince, Lawrence S, Sahoo, Debashis
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 08.04.2020
• Subjects: biomarker; Boolean analysis; CAD; gene expression; macrophage; Physiology; macrophage; biomarker; Boolean analysis; gene expression; CAD
• ISSN: 1664-042X; 1664-042X
• DOI: 10.3389/fphys.2020.00275

Macrophages engulf and digest microbes, cellular debris, and various disease-associated cells throughout the body. Understanding the dynamics of macrophage gene expression is crucial for studying human diseases. As both bulk RNAseq and single cell RNAseq datasets become more numerous and complex, identifying a universal and reliable marker of macrophage cell becomes paramount. Traditional approaches have relied upon tissue specific expression patterns. To identify universal biomarkers of macrophage, we used a previously published computational approach called BECC (Boolean Equivalent Correlated Clusters) that was originally used to identify conserved cell cycle genes. We performed BECC analysis using the known macrophage marker CD14 as a seed gene. The main idea behind BECC is that it uses massive database of public gene expression dataset to establish robust co-expression patterns identified using a combination of correlation, linear regression and Boolean equivalences. Our analysis identified and validated FCER1G and TYROBP as novel universal biomarkers for macrophages in human and mouse tissues.