This is basically a descriptive report of results obtained after searching a single database, the Sbisa et al. 2007 dataset, for ribosomal proteins. The information given is too incomplete to judge the significance of the findings, and no statistics are performed to back up claims of trends in the data.
1) Is the presence of an RE as defined in that particular database actually a good prior indicator of regulation by p53 etc. as is claimed? The reader should not have to do their own search, or take it on faith, to find out how reliable this is as a proxy indicator for actual p53-mediated regulation. In addition, that resource is 8 years old, and there is now abundant ChIP data on p53, so why was this not used to filter the REs, at least for ability to bind p53?
2) No information was given on the overall proportions of genes that were regulated in the microarray data or that were classed as RE-containing. A full contingency table of gene numbers both within and without each classification (RP +/-; RE-containing +/-; p53 regulated +/-/NA) is needed to judge how significant the numbers in Fig1 really are. I am not requiring that they prove that RPs are over-represented in p53 targets, as clearly the point of this is to demonstrate that RP genes, which are considered ‘housekeeping’ genes by some, undergo just as much regulatory control as other categories of genes; but not necessarily more regulation. Nonetheless they need to present the numbers in the negative categories so the reader can have some basis for comparison.
3) "The expression trend (either an upregulation or a downregulation) for a given RP gene is similar across various p53 family overexpression (Supplementary Table 1)" I cannot see this table. However some statistical analysis is required to make this statement.
4) “Nevertheless, the coincidence in RP gene expression trend across cell lines” What is the likelihood that this correlation would occur by chance if there were no genuine trend? Again, there is no statistical test, at least not that I can see without access to this supplementary table.
5) "an overwhelming number, 9 out of 12 eIF genes that have p53 RE and respond to p53 overexpression, were found to be downregulated". 9 of 12 is quite likely to occur by chance in a coin-toss, this is not overwhelming, please change the wording.