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Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans

Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Shogoinkawahara-cho, Kyoto 606-8507, Japan
Department of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, Japan
Research Department, Ono Pharmaceutical Co., Ltd., Kyutaromachi, Osaka 618-8585, Japan
Department of Pharmacology, Faculty of medicine, Yamagata University, Iida-Nishi, Yamagata 990-9585, Japan
Author to whom correspondence should be addressed.
Academic Editor: Pietro Scicchitano
Biomolecules 2022, 12(6), 859;
Received: 31 March 2022 / Revised: 16 June 2022 / Accepted: 17 June 2022 / Published: 20 June 2022
(This article belongs to the Special Issue Molecular Pathogenesis of Cardiac Arrhythmia)
The heart is a significant organ in mammalian life, and the heartbeat mechanism has been an essential 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. Here, we analyzed transcriptome data in mouse, rat, and human atria, ventricles, and sinoatrial nodes (SA) obtained from different platforms and compared them by calculating specificity measure (SPM) values in consideration of species differences. Among the three heart regions, the species differences in SA were the greatest, and we searched for genes that determined the essential characteristics of SA, which was SHOX2 in our criteria. The SPM value of SHOX2 was prominently high across species. 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. This study identified the importance of SHOX2 as an SA-specific transcription factor, a novel cardiac regional marker, and species-dependent ontologies. View Full-Text
Keywords: transcriptome; heart; SHOX2 transcriptome; heart; SHOX2
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MDPI and ACS Style

Okada, D.; Okamoto, Y.; Io, T.; Oka, M.; Kobayashi, D.; Ito, S.; Yamada, R.; Ishii, K.; Ono, K. Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans. Biomolecules 2022, 12, 859.

AMA Style

Okada D, Okamoto Y, Io T, Oka M, Kobayashi D, Ito S, Yamada R, Ishii K, Ono K. Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans. Biomolecules. 2022; 12(6):859.

Chicago/Turabian Style

Okada, Daigo, Yosuke Okamoto, Toshiro Io, Miho Oka, Daiki Kobayashi, Suzuka Ito, Ryo Yamada, Kuniaki Ishii, and Kyoichi Ono. 2022. "Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans" Biomolecules 12, no. 6: 859.

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