miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems
| العنوان: | miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems |
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| المؤلفون: | Fabian Kern, Tobias Fehlmann, Christina Backes, Nadja Grammes, Kendall Van Keuren-Jensen, Eckart Meese, Louisa Schwed, Jeffrey Solomon, David Craig, Andreas Keller |
| المصدر: | Nucleic Acids Research |
| بيانات النشر: | Oxford University Press (OUP), 2020. |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | AcademicSubjects/SCI00010, Breast Neoplasms, Computational biology, Biology, MiRBase, Workflow, Set (abstract data type), Mice, 03 medical and health sciences, Annotation, 0302 clinical medicine, Software, Genetics, Animals, Humans, Carcinoma, Renal Cell, 030304 developmental biology, computer.programming_language, 0303 health sciences, Application programming interface, business.industry, Parkinson Disease, Python (programming language), Kidney Neoplasms, MicroRNAs, 030220 oncology & carcinogenesis, Web Server Issue, Disease Progression, Female, business, computer, Biomarkers, Workflow management system |
| الوصف: | Gene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs. Here, we present miEAA 2.0, supporting miRNA input from ten frequently investigated organisms. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miRBase miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualizations such as heatmaps and running sum curves with background distributions. We demonstrate the new features with case studies for human kidney cancer, a biomarker study on Parkinson’s disease from the PPMI cohort, and a mouse model for breast cancer. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2Test. |
| تدمد: | 1362-4962 0305-1048 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::62e695c9e997a6bacfd256eeb91e171dTest https://doi.org/10.1093/nar/gkaa309Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....62e695c9e997a6bacfd256eeb91e171d |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 13624962 03051048 |
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