Identification of key genes in SARS-CoV-2 patients on bioinformatics analysis
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Abstract
The COVID-19 pandemic has infected millions of people and overwhelmed many health systems globally. Our study is to identify differentially expressed genes (DEGs) and associated biological processes of COVID-19 using a bioinformatics approach to elucidate their potential pathogenesis. The gene expression profiles of the GSE152075 datasets were originally produced by using the high-throughput Illumina NextSeq 500. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed to identify functional categories and biochemical pathways. GO and KEGG results suggested that several biological pathways such as “Fatty acid metabolism” and “Cilium morphogenesis” are mostly involved in the development of COVID-19. Moreover, several genes are critical for virus invasion and adhesion including FLOC, DYNLL1, FBXL3, and FBXW11 and show significant differences in COVID-19 patients. Thus, our study provides further insights into the underlying pathogenesis of COVID-19.
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SciScore for 10.1101/2020.08.09.243444: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Methods Data resources Gene expression profile dataset GSE152075 was obtained from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). http://www.ncbi.nlm.nih.gov/geo/suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)GO analysis and KEGG pathway enrichment analysis of DEGs in our study were analyzed by the Database for Annotation, Visualization, and … SciScore for 10.1101/2020.08.09.243444: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Methods Data resources Gene expression profile dataset GSE152075 was obtained from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). http://www.ncbi.nlm.nih.gov/geo/suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)GO analysis and KEGG pathway enrichment analysis of DEGs in our study were analyzed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID) (http://david.ncifcrf.gov/) online tools. KEGGsuggested: (KEGG, RRID:SCR_012773)DAVIDsuggested: (DAVID, RRID:SCR_001881)The significant modules were from the constructed PPI network using MCODE. MCODEsuggested: (MCODE, RRID:SCR_015828)PPI network analysis of DEGs To further explore the relationships of GGEs at the protein level, the PPI networks were constructed by using the Cytoscape software. Cytoscapesuggested: (Cytoscape, RRID:SCR_003032)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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SciScore for 10.1101/2020.08.09.243444: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources resources: Gene expression profile dataset GSE152075 was obtained from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). http://www.ncbi.nlm.nih.gov/geo/suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)(KEGG) database is commonly used for systematic analysis of gene functions and annotation of biological pathways. KEGGsuggested: (KEGG, RRID:SCR_012773)GO analysis and KEGG pathway enrichment analysis of DEGs in our study were analyzed by the Database for Annotation, … SciScore for 10.1101/2020.08.09.243444: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources resources: Gene expression profile dataset GSE152075 was obtained from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). http://www.ncbi.nlm.nih.gov/geo/suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)(KEGG) database is commonly used for systematic analysis of gene functions and annotation of biological pathways. KEGGsuggested: (KEGG, RRID:SCR_012773)GO analysis and KEGG pathway enrichment analysis of DEGs in our study were analyzed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID) (http://david.ncifcrf.gov/) online tools. DAVIDsuggested: (DAVID, RRID:SCR_001881)The significant modules were from the constructed PPI network using MCODE. MCODEsuggested: (MCODE, RRID:SCR_015828)the functional and pathway enrichment analyses were performed using Reactome Pathway Database (https://reactome.org/). Reactome Pathway Databasesuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
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