Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans
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 spe...
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| Format: | Article |
| Jezik: | English |
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MDPI AG
2022-06-01
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| Serija: | Biomolecules |
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| Online dostop: | https://www.mdpi.com/2218-273X/12/6/859 |
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| author | Daigo Okada Yosuke Okamoto Toshiro Io Miho Oka Daiki Kobayashi Suzuka Ito Ryo Yamada Kuniaki Ishii Kyoichi Ono |
| author_facet | Daigo Okada Yosuke Okamoto Toshiro Io Miho Oka Daiki Kobayashi Suzuka Ito Ryo Yamada Kuniaki Ishii Kyoichi Ono |
| author_sort | Daigo Okada |
| collection | DOAJ |
| description | 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 <i>SHOX2</i> in our criteria. The SPM value of <i>SHOX2</i> 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 <i>SHOX2</i> as an SA-specific transcription factor, a novel cardiac regional marker, and species-dependent ontologies. |
| first_indexed | 2024-03-10T00:17:50Z |
| format | Article |
| id | doaj.art-4f8d9f3ba4b64a11a0a6fc9ad1c4400c |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T00:17:50Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-4f8d9f3ba4b64a11a0a6fc9ad1c4400c2023-11-23T15:48:12ZengMDPI AGBiomolecules2218-273X2022-06-0112685910.3390/biom12060859Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and HumansDaigo Okada0Yosuke Okamoto1Toshiro Io2Miho Oka3Daiki Kobayashi4Suzuka Ito5Ryo Yamada6Kuniaki Ishii7Kyoichi Ono8Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Shogoinkawahara-cho, Kyoto 606-8507, JapanDepartment of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, JapanResearch Department, Ono Pharmaceutical Co., Ltd., Kyutaromachi, Osaka 618-8585, JapanResearch Department, Ono Pharmaceutical Co., Ltd., Kyutaromachi, Osaka 618-8585, JapanDepartment of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, JapanDepartment of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, JapanCenter for Genomic Medicine, Graduate School of Medicine, Kyoto University, Shogoinkawahara-cho, Kyoto 606-8507, JapanDepartment of Pharmacology, Faculty of medicine, Yamagata University, Iida-Nishi, Yamagata 990-9585, JapanDepartment of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, JapanThe 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 <i>SHOX2</i> in our criteria. The SPM value of <i>SHOX2</i> 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 <i>SHOX2</i> as an SA-specific transcription factor, a novel cardiac regional marker, and species-dependent ontologies.https://www.mdpi.com/2218-273X/12/6/859transcriptomeheartSHOX2 |
| spellingShingle | Daigo Okada Yosuke Okamoto Toshiro Io Miho Oka Daiki Kobayashi Suzuka Ito Ryo Yamada Kuniaki Ishii Kyoichi Ono Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans Biomolecules transcriptome heart SHOX2 |
| title | Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans |
| title_full | Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans |
| title_fullStr | Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans |
| title_full_unstemmed | Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans |
| title_short | Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans |
| title_sort | comparative study of transcriptome in the hearts isolated from mice rats and humans |
| topic | transcriptome heart SHOX2 |
| url | https://www.mdpi.com/2218-273X/12/6/859 |
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