Data-Driven Insights into the Association Between Oxidative Stress and Calcium-Regulating Proteins in Cardiovascular Disease
A growing body of biomedical literature suggests a bidirectional regulatory relationship between cardiac calcium (Ca<sup>2+</sup>)-regulating proteins and reactive oxygen species (ROS) that is integral to the pathogenesis of various cardiac disorders via oxidative stress (OS) signaling....
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MDPI AG
2024-11-01
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| Series: | Antioxidants |
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| Online Access: | https://www.mdpi.com/2076-3921/13/11/1420 |
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| author | Namuna Panday Dibakar Sigdel Irsyad Adam Joseph Ramirez Aarushi Verma Anirudh N. Eranki Wei Wang Ding Wang Peipei Ping |
| author_facet | Namuna Panday Dibakar Sigdel Irsyad Adam Joseph Ramirez Aarushi Verma Anirudh N. Eranki Wei Wang Ding Wang Peipei Ping |
| author_sort | Namuna Panday |
| collection | DOAJ |
| description | A growing body of biomedical literature suggests a bidirectional regulatory relationship between cardiac calcium (Ca<sup>2+</sup>)-regulating proteins and reactive oxygen species (ROS) that is integral to the pathogenesis of various cardiac disorders via oxidative stress (OS) signaling. To address the challenge of finding hidden connections within the growing volume of biomedical research, we developed a data science pipeline for efficient data extraction, transformation, and loading. Employing the CaseOLAP (Context-Aware Semantic Analytic Processing) algorithm, our pipeline quantifies interactions between 128 human cardiomyocyte Ca<sup>2+</sup>-regulating proteins and eight cardiovascular disease (CVD) categories. Our machine-learning analysis of CaseOLAP scores reveals that the molecular interfaces of Ca<sup>2+</sup>-regulating proteins uniquely associate with cardiac arrhythmias and diseases of the cardiac conduction system, distinguishing them from other CVDs. Additionally, a knowledge graph analysis identified 59 of the 128 Ca<sup>2+</sup>-regulating proteins as involved in OS-related cardiac diseases, with cardiomyopathy emerging as the predominant category. By leveraging a link prediction algorithm, our research illuminates the interactions between Ca<sup>2+</sup>-regulating proteins, OS, and CVDs. The insights gained from our study provide a deeper understanding of the molecular interplay between cardiac ROS and Ca<sup>2+</sup>-regulating proteins in the context of CVDs. Such an understanding is essential for the innovation and development of targeted therapeutic strategies. |
| format | Article |
| id | doaj-art-28c5757799d14504aeb565e6ee2a8a9e |
| institution | OA Journals |
| issn | 2076-3921 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Antioxidants |
| spelling | doaj-art-28c5757799d14504aeb565e6ee2a8a9e2025-08-20T02:07:57ZengMDPI AGAntioxidants2076-39212024-11-011311142010.3390/antiox13111420Data-Driven Insights into the Association Between Oxidative Stress and Calcium-Regulating Proteins in Cardiovascular DiseaseNamuna Panday0Dibakar Sigdel1Irsyad Adam2Joseph Ramirez3Aarushi Verma4Anirudh N. Eranki5Wei Wang6Ding Wang7Peipei Ping8Department of Physiology, School of Medicine, University of California, Los Angeles, CA 90095, USADepartment of Physiology, School of Medicine, University of California, Los Angeles, CA 90095, USANHLBI Integrated Cardiovascular Data Science Training Program (iDISCOVER), University of California, Los Angeles, CA 90095, USANHLBI Integrated Cardiovascular Data Science Training Program (iDISCOVER), University of California, Los Angeles, CA 90095, USANHLBI Integrated Cardiovascular Data Science Training Program (iDISCOVER), University of California, Los Angeles, CA 90095, USANHLBI Integrated Cardiovascular Data Science Training Program (iDISCOVER), University of California, Los Angeles, CA 90095, USADepartment of Computer Science, University of California, Los Angeles, CA 90095, USADepartment of Physiology, School of Medicine, University of California, Los Angeles, CA 90095, USADepartment of Physiology, School of Medicine, University of California, Los Angeles, CA 90095, USAA growing body of biomedical literature suggests a bidirectional regulatory relationship between cardiac calcium (Ca<sup>2+</sup>)-regulating proteins and reactive oxygen species (ROS) that is integral to the pathogenesis of various cardiac disorders via oxidative stress (OS) signaling. To address the challenge of finding hidden connections within the growing volume of biomedical research, we developed a data science pipeline for efficient data extraction, transformation, and loading. Employing the CaseOLAP (Context-Aware Semantic Analytic Processing) algorithm, our pipeline quantifies interactions between 128 human cardiomyocyte Ca<sup>2+</sup>-regulating proteins and eight cardiovascular disease (CVD) categories. Our machine-learning analysis of CaseOLAP scores reveals that the molecular interfaces of Ca<sup>2+</sup>-regulating proteins uniquely associate with cardiac arrhythmias and diseases of the cardiac conduction system, distinguishing them from other CVDs. Additionally, a knowledge graph analysis identified 59 of the 128 Ca<sup>2+</sup>-regulating proteins as involved in OS-related cardiac diseases, with cardiomyopathy emerging as the predominant category. By leveraging a link prediction algorithm, our research illuminates the interactions between Ca<sup>2+</sup>-regulating proteins, OS, and CVDs. The insights gained from our study provide a deeper understanding of the molecular interplay between cardiac ROS and Ca<sup>2+</sup>-regulating proteins in the context of CVDs. Such an understanding is essential for the innovation and development of targeted therapeutic strategies.https://www.mdpi.com/2076-3921/13/11/1420Ca<sup>2+</sup>-regulating proteinsoxidative stressreactive oxygen speciescardiovascular diseasestext miningknowledge graph |
| spellingShingle | Namuna Panday Dibakar Sigdel Irsyad Adam Joseph Ramirez Aarushi Verma Anirudh N. Eranki Wei Wang Ding Wang Peipei Ping Data-Driven Insights into the Association Between Oxidative Stress and Calcium-Regulating Proteins in Cardiovascular Disease Antioxidants Ca<sup>2+</sup>-regulating proteins oxidative stress reactive oxygen species cardiovascular diseases text mining knowledge graph |
| title | Data-Driven Insights into the Association Between Oxidative Stress and Calcium-Regulating Proteins in Cardiovascular Disease |
| title_full | Data-Driven Insights into the Association Between Oxidative Stress and Calcium-Regulating Proteins in Cardiovascular Disease |
| title_fullStr | Data-Driven Insights into the Association Between Oxidative Stress and Calcium-Regulating Proteins in Cardiovascular Disease |
| title_full_unstemmed | Data-Driven Insights into the Association Between Oxidative Stress and Calcium-Regulating Proteins in Cardiovascular Disease |
| title_short | Data-Driven Insights into the Association Between Oxidative Stress and Calcium-Regulating Proteins in Cardiovascular Disease |
| title_sort | data driven insights into the association between oxidative stress and calcium regulating proteins in cardiovascular disease |
| topic | Ca<sup>2+</sup>-regulating proteins oxidative stress reactive oxygen species cardiovascular diseases text mining knowledge graph |
| url | https://www.mdpi.com/2076-3921/13/11/1420 |
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