Comparative study of transcriptome in the hearts isolated from mice, rats, and human

The heart is a major organ in mammalian life, and the study of transcription factors, particularly those that regulate cardiac rhythm, has been an important focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that determine species differences. In this study, we reanalyzed mouse, rat, and human transcriptome data obtained from different platforms by calculating specificity measure (SPM) values in consideration of species differences. SHOX2 and HOXA2 were found to be important as sinoatrial node-specific transcription factors throughout the species. In particular, the SPM value of SHOX2 is very high. Similarly, by calculating SPM values, we identified 3 atrial-specific, 11 ventricular-specific, and 17 SA-specific markers. Ontology analysis identified 70 cardiac region- and species-specific ontologies. These results suggest that reanalyzing existing data by calculating SPM values may identify novel tissue-specific genes and species-dependent gene expression. Within this study, we identified the importance of SHOX2 as a SA-specific transcription factor, a novel cardiac regional marker, and ontologies. Total RNA from sinoatrial nodes and left and right ventricles and atria were examined using Illumina mouse Ref-8 microarrays (N = 4 for each of the five groups).