Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis
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SciScore for 10.1101/2020.04.09.033910: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Human-SARS-CoV-2 interactome data acquisition: To build human interactome, we assembled a comprehensive protein-protein interactions (PPIs) comprising experimentally validated PPIs from STRING database32 and four additional proteomes-scale interactome studies i.e. Human Interactome I and II, BioPlex, QUBIC, and CoFrac (reviewed in33. STRINGsuggested: (STRING, RRID:SCR_005223)BioPlexsuggested: (BioPlex, RRID:SCR_016144)Briefly, GEO2R utilizes limma R package. GEO2Rsuggested: (GEO2R, RRID:SCR_016569)limmasuggested: (LIMMA, RRID:SCR_010943)Network topology analyses was performed using … SciScore for 10.1101/2020.04.09.033910: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Human-SARS-CoV-2 interactome data acquisition: To build human interactome, we assembled a comprehensive protein-protein interactions (PPIs) comprising experimentally validated PPIs from STRING database32 and four additional proteomes-scale interactome studies i.e. Human Interactome I and II, BioPlex, QUBIC, and CoFrac (reviewed in33. STRINGsuggested: (STRING, RRID:SCR_005223)BioPlexsuggested: (BioPlex, RRID:SCR_016144)Briefly, GEO2R utilizes limma R package. GEO2Rsuggested: (GEO2R, RRID:SCR_016569)limmasuggested: (LIMMA, RRID:SCR_010943)Network topology analyses was performed using NetworkX66 (version 2.4) Python (version 3.7.6) package was used except weighted k-shell-decomposition for which we downloaded wk-shell-decomposition Cystoscope App (version 1.0). Pythonsuggested: (IPython, RRID:SCR_001658)Cytoscape (Version 7.3.2) was used to visualize all the networks. Cytoscapesuggested: (Cytoscape, RRID:SCR_003032)Gene Ontology Functional Enrichment Analysis: The functional enrichment analysis was done by Kyoto Encyclopedia of Genes and Genomes (KEGG) KEGGsuggested: (KEGG, RRID:SCR_012773), ingenuity pathway analysis (IPA), WikiPathways, GO biological process, ClueGO, and enricher for human phenotype ontology and rare diseases term with their statistically significant parameters67. ingenuity pathway analysissuggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)WikiPathwayssuggested: (WikiPathways, RRID:SCR_002134)ClueGOsuggested: (ClueGO, RRID:SCR_005748)Results from OddPub: Thank you for sharing your data.
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: Please consider improving the rainbow (“jet”) colormap(s) used on page 39. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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