Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response
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SciScore for 10.1101/2020.03.26.009605: (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. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Data consisted on the quantification of 6381 proteins in human Caco-2 cell secretomes at four time points after infection with SARS-CoV-2 virus. Caco-2suggested: NoneSoftware and Algorithms Sentences Resources Data was analyzed in the context of pathways obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (Release 90.0+/05-29, May 2019). KEGGsuggested: (KEGG, RRID:SCR_012773)iPathwayGuide was also used for network … SciScore for 10.1101/2020.03.26.009605: (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. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Data consisted on the quantification of 6381 proteins in human Caco-2 cell secretomes at four time points after infection with SARS-CoV-2 virus. Caco-2suggested: NoneSoftware and Algorithms Sentences Resources Data was analyzed in the context of pathways obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (Release 90.0+/05-29, May 2019). KEGGsuggested: (KEGG, RRID:SCR_012773)iPathwayGuide was also used for network analysis, using String v11.0 Jan 2019 and BioGRID v3.5.171 Mar 2019 as data sources. Stringsuggested: (STRING, RRID:SCR_005223)BioGRIDsuggested: (BioGrid Australia, RRID:SCR_006334)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 TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- No funding statement was detected.
- No protocol registration statement was detected.
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