PONE-D-22-19814The relationship of mRNA with protein expression in CD8+ T cells associates with gene class and gene characteristicsPLOS ONE

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Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: In “The relationship of mRNA with protein expression in CD8+ T cells associates with gene class and gene characteristics”, Nicolet et. al performed bioinformatic analyses of previously published RNA and protein data from primary human CD8+ T cells. They demonstrate, as has been reported in other contexts, poor correlation between RNA and proteins levels. They furthered their analyses by demonstrating unique correlation patterns between different classes of genes. Overall, this study is scientifically sound, and despite being almost purely in silico, it represents useful data that should be published and available to the field. My concerns are relatively minor, mostly aimed at ensuring clarity in the results:

1) The activated cells were treated with Monensin. Can the authors present data or citations as to whether Monensin impacts protein and/or RNA levels?

2) In figure 4 the authors examine RNA/protein levels when stratifying gene based on various characteristics, such as conservation or UTR length. In Fig 3 they show that genes within each class can have wide ranges for these values. If the authors performed a similar analysis as Fig 4, except grouping the data by gene class, are the trends reported in Figure 4 consistent between each class?

Reviewer #2: The authors have not thought much on the appropriate statistical analysis/test to run, in particular with the regression analysis. Data could have been transformed and presented better. For example, using box plots. See the attached document for comprehensive comments on the manuscript.

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-22-19814_ReviewerComments.pdf

The relationship of mRNA with protein expression in CD8+ T cells associates with gene class and gene characteristics

PONE-D-22-19814R1

Dear Dr. Wolkers,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Alexander F. Palazzo, Ph.D.

Academic Editor

PLOS ONE

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