Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications
RNA sequencing (RNA-seq) has emerged as a prominent resource for transcriptomic analysis due to its ability to measure gene expression in a highly sensitive and accurate manner. With the increasing availability of RNA-seq data analysis from clinical studies and patient samples, the development of ef...
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2025-01-01
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| author | Farhana Manzoor Cyruss A. Tsurgeon Vibhuti Gupta |
| author_facet | Farhana Manzoor Cyruss A. Tsurgeon Vibhuti Gupta |
| author_sort | Farhana Manzoor |
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| description | RNA sequencing (RNA-seq) has emerged as a prominent resource for transcriptomic analysis due to its ability to measure gene expression in a highly sensitive and accurate manner. With the increasing availability of RNA-seq data analysis from clinical studies and patient samples, the development of effective visualization tools for RNA-seq analysis has become increasingly important to help clinicians and biomedical researchers better understand the complex patterns of gene expression associated with health and disease. This review aims to outline the current state-of-the-art data visualization techniques and tools commonly used to frame clinical inferences from RNA-seq data and point out their benefits, applications, and limitations. A systematic review of English articles using PubMed, Scopus, Web of Science, and IEEE Xplore databases was performed. Search terms included “RNA-seq”, “visualization”, “plots”, and “clinical”. Only full-text studies reported between 2017 and 2024 were included for analysis. Following PRISMA guidelines, a total of 126 studies were identified, of which 33 studies met the inclusion criteria. We found that 18% of studies have visualization techniques and tools for circular RNA-seq data, 56% for single-cell RNA-seq data, 23% for bulk RNA-seq data, and 3% for long non-coding RNA-seq data. Overall, this review provides a comprehensive overview of the common visualization tools and their potential applications, which is a useful resource for researchers and clinicians interested in using RNA-seq data for various clinical purposes (e.g., diagnosis or prognosis). |
| format | Article |
| id | doaj-art-a2eb84e354b3411793fd80f6269169a5 |
| institution | Kabale University |
| issn | 2306-5354 |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-a2eb84e354b3411793fd80f6269169a52025-01-24T13:23:06ZengMDPI AGBioengineering2306-53542025-01-011215610.3390/bioengineering12010056Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical ApplicationsFarhana Manzoor0Cyruss A. Tsurgeon1Vibhuti Gupta2Department of Computer Science and Data Science, School of Applied Computational Sciences, Meharry Medical College, Nashville, TN 37208, USADepartment of Biomedical Data Science, School of Applied Computational Sciences, Meharry Medical College, Nashville, TN 37208, USADepartment of Computer Science and Data Science, School of Applied Computational Sciences, Meharry Medical College, Nashville, TN 37208, USARNA sequencing (RNA-seq) has emerged as a prominent resource for transcriptomic analysis due to its ability to measure gene expression in a highly sensitive and accurate manner. With the increasing availability of RNA-seq data analysis from clinical studies and patient samples, the development of effective visualization tools for RNA-seq analysis has become increasingly important to help clinicians and biomedical researchers better understand the complex patterns of gene expression associated with health and disease. This review aims to outline the current state-of-the-art data visualization techniques and tools commonly used to frame clinical inferences from RNA-seq data and point out their benefits, applications, and limitations. A systematic review of English articles using PubMed, Scopus, Web of Science, and IEEE Xplore databases was performed. Search terms included “RNA-seq”, “visualization”, “plots”, and “clinical”. Only full-text studies reported between 2017 and 2024 were included for analysis. Following PRISMA guidelines, a total of 126 studies were identified, of which 33 studies met the inclusion criteria. We found that 18% of studies have visualization techniques and tools for circular RNA-seq data, 56% for single-cell RNA-seq data, 23% for bulk RNA-seq data, and 3% for long non-coding RNA-seq data. Overall, this review provides a comprehensive overview of the common visualization tools and their potential applications, which is a useful resource for researchers and clinicians interested in using RNA-seq data for various clinical purposes (e.g., diagnosis or prognosis).https://www.mdpi.com/2306-5354/12/1/56RNA-seqsequencingvisualization |
| spellingShingle | Farhana Manzoor Cyruss A. Tsurgeon Vibhuti Gupta Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications Bioengineering RNA-seq sequencing visualization |
| title | Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications |
| title_full | Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications |
| title_fullStr | Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications |
| title_full_unstemmed | Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications |
| title_short | Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications |
| title_sort | exploring rna seq data analysis through visualization techniques and tools a systematic review of opportunities and limitations for clinical applications |
| topic | RNA-seq sequencing visualization |
| url | https://www.mdpi.com/2306-5354/12/1/56 |
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