دورية أكاديمية
Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data.
| العنوان: | Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data. |
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| المؤلفون: | Macedo-da-Silva J; GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil., Coutinho JVP; GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil., Rosa-Fernandes L; GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil., Marie SKN; Cellular and Molecular Biology Laboratory (LIM 15), Neurology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil., Palmisano G; GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil; School of Natural Sciences, Macquarie University, Sydney, NSW, Australia. Electronic address: palmisano.gp@gmail.com. |
| المصدر: | Advances in protein chemistry and structural biology [Adv Protein Chem Struct Biol] 2022; Vol. 131, pp. 311-339. Date of Electronic Publication: 2022 May 12. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Elsevier Country of Publication: Netherlands NLM ID: 101497281 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1876-1631 (Electronic) Linking ISSN: 18761623 NLM ISO Abbreviation: Adv Protein Chem Struct Biol Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Amsterdam : Elsevier |
| مواضيع طبية MeSH: | COVID-19*/genetics, Computational Biology ; Humans ; Proteome/metabolism ; Proteomics/methods ; SARS-CoV-2/genetics |
| مستخلص: | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in late 2019 in Wuhan, China, and has proven to be highly pathogenic, making it a global public health threat. The immediate need to understand the mechanisms and impact of the virus made omics techniques stand out, as they can offer a holistic and comprehensive view of thousands of molecules in a single experiment. Mastering bioinformatics tools to process, analyze, integrate, and interpret omics data is a powerful knowledge to enrich results. We present a robust and open access computational pipeline for extracting information from quantitative proteomics and transcriptomics public data. We present the entire pipeline from raw data to differentially expressed genes. We explore processes and pathways related to mapped transcripts and proteins. A pipeline is presented to integrate and compare proteomics and transcriptomics data using also packages available in the Bioconductor and providing the codes used. Cholesterol metabolism, immune system activity, ECM, and proteasomal degradation pathways increased in infected patients. Leukocyte activation profile was overrepresented in both proteomics and transcriptomics data. Finally, we found a panel of proteins and transcripts regulated in the same direction in the lung transcriptome and plasma proteome that distinguish healthy and infected individuals. This panel of markers was confirmed in another cohort of patients, thus validating the robustness and functionality of the tools presented. (Copyright © 2022 Elsevier Inc. All rights reserved.) |
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| فهرسة مساهمة: | Keywords: COVID-19; Data integration; Proteomics; SARS-CoV-2; Transcriptomics |
| المشرفين على المادة: | 0 (Proteome) |
| تواريخ الأحداث: | Date Created: 20220725 Date Completed: 20220726 Latest Revision: 20240909 |
| رمز التحديث: | 20240909 |
| مُعرف محوري في PubMed: | PMC9095070 |
| DOI: | 10.1016/bs.apcsb.2022.04.002 |
| PMID: | 35871895 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1876-1631 |
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| DOI: | 10.1016/bs.apcsb.2022.04.002 |