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A beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration
The discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains an active area of research. To boost these efforts, we demonstrate the utility of publicly available datasets for probing the pathogenic relevance of candidate markers in NDDs. As a sta...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10325954/ https://www.ncbi.nlm.nih.gov/pubmed/37414779 http://dx.doi.org/10.1038/s41597-023-02338-1 |
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author | Gomes Moreira, Diana Jan, Asad |
author_facet | Gomes Moreira, Diana Jan, Asad |
author_sort | Gomes Moreira, Diana |
collection | PubMed |
description | The discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains an active area of research. To boost these efforts, we demonstrate the utility of publicly available datasets for probing the pathogenic relevance of candidate markers in NDDs. As a starting point, we introduce the readers to several open access resources, which contain gene expression profiles and proteomics datasets from patient studies in common NDDs, including proteomics analyses of cerebrospinal fluid (CSF). Then, we illustrate the method for curated gene expression analyses across select brain regions from four cohorts of Parkinson disease patients (and from one study in common NDDs), probing glutathione biogenesis, calcium signaling and autophagy. These data are complemented by findings of select markers in CSF-based studies in NDDs. Additionally, we enclose several annotated microarray studies, and summarize reports on CSF proteomics across the NDDs, which the readers can utilize for translational purposes. We anticipate that this “beginner’s guide” will benefit the research community in NDDs, and would serve as a useful educational tool. |
format | Online Article Text |
id | pubmed-10325954 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-103259542023-07-08 A beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration Gomes Moreira, Diana Jan, Asad Sci Data Analysis The discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains an active area of research. To boost these efforts, we demonstrate the utility of publicly available datasets for probing the pathogenic relevance of candidate markers in NDDs. As a starting point, we introduce the readers to several open access resources, which contain gene expression profiles and proteomics datasets from patient studies in common NDDs, including proteomics analyses of cerebrospinal fluid (CSF). Then, we illustrate the method for curated gene expression analyses across select brain regions from four cohorts of Parkinson disease patients (and from one study in common NDDs), probing glutathione biogenesis, calcium signaling and autophagy. These data are complemented by findings of select markers in CSF-based studies in NDDs. Additionally, we enclose several annotated microarray studies, and summarize reports on CSF proteomics across the NDDs, which the readers can utilize for translational purposes. We anticipate that this “beginner’s guide” will benefit the research community in NDDs, and would serve as a useful educational tool. Nature Publishing Group UK 2023-07-06 /pmc/articles/PMC10325954/ /pubmed/37414779 http://dx.doi.org/10.1038/s41597-023-02338-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Analysis Gomes Moreira, Diana Jan, Asad A beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration |
title | A beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration |
title_full | A beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration |
title_fullStr | A beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration |
title_full_unstemmed | A beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration |
title_short | A beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration |
title_sort | beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration |
topic | Analysis |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10325954/ https://www.ncbi.nlm.nih.gov/pubmed/37414779 http://dx.doi.org/10.1038/s41597-023-02338-1 |
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