RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
No abstract available
Article activity feed
-
-
SciScore for 10.1101/2020.04.28.065201: (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
Experimental Models: Cell Lines Sentences Resources Both RNA-GPS and the GRU model are trained and tuned on the same APEX-seq data, measuring localization within HEK293T cells (Fazal et al., 2019), using identical data splits of 80% train, 10% validation, and 10% train. HEK293Tsuggested: NoneSoftware and Algorithms Sentences Resources Obtaining viral genomes: SARS-CoV-2 viral genomes were programmatically queried from the GenBank online database using the BioPython library’s Entrez module (Cock et al., 2009). BioPythonsuggested: (Biopython, RRID:SCR_007173)Plotting and additional metrics: All plots were generated using a combination of … SciScore for 10.1101/2020.04.28.065201: (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
Experimental Models: Cell Lines Sentences Resources Both RNA-GPS and the GRU model are trained and tuned on the same APEX-seq data, measuring localization within HEK293T cells (Fazal et al., 2019), using identical data splits of 80% train, 10% validation, and 10% train. HEK293Tsuggested: NoneSoftware and Algorithms Sentences Resources Obtaining viral genomes: SARS-CoV-2 viral genomes were programmatically queried from the GenBank online database using the BioPython library’s Entrez module (Cock et al., 2009). BioPythonsuggested: (Biopython, RRID:SCR_007173)Plotting and additional metrics: All plots were generated using a combination of seaborn and matplotlib Python packages (Hunter, 2007). Pythonsuggested: (IPython, RRID:SCR_001658)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:One limitation of our work lies within its attempt to generalize models trained on human RNA transcript localization data, to transcripts derived from a different species. A model learned on HEK293T cells also may not be an appropriate model for cell types that are infected by SARS-CoV-2. Although the sharing of biological machinery between human cells and SARS-CoV-2 coupled with RNA-GPS’s strong performance on held-out test datasets leads us to believe that this approach is promising, viral infection also substantially remodels the cell’s internal machinery, and the expression of viral RNA binding proteins (not accounted for in our model) can both introduce errors into our predictions. Thus, localization experiments are necessary to validate our computational analyses. Cross-referencing our results against existing literature is somewhat limited, as most studies have focused on the localization of viral proteins rather than viral transcripts. Furthermore, RNA localization is undoubtedly one of many pieces of complex, interconnected mechanisms that this coronavirus adopts, and our hypotheses presented here do not preclude (many) additional critical biological phenomena. In summary, we build upon recent computational models of RNA subcellular localization to study, in silico, the localization properties of SARS-CoV-2. Our results suggest that nuclear-mitochondrial transcript localization patterns may be an important, unique characteristic of SARS-CoV-2 that warrants additional...
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.
- 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.
-
