iRNAm5C-PseDNC: identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide composition

Abstract

Occurring at cytosine (C) of RNA, 5-methylcytosine (m5C) is an important post-transcriptional modification (PTCM). The modification plays significant roles in biological processes by regulating RNA metabolism in both eukaryotes and prokaryotes. It may also, however, cause cancers and other major diseases. Given an uncharacterized RNA sequence that contains many C residues, can we identify which one of them can be of m5C modification, and which one cannot? It is no doubt a crucial problem, particularly with the explosive growth of RNA sequences in the postgenomic age. Unfortunately, so far no user-friendly web-server whatsoever has been developed to address such a problem. To meet the increasingly high demand from most experimental scientists working in the area of drug development, we have developed a new predictor called iRNAm5C-PseDNC by incorporating ten types of physical-chemical properties into pseudo dinucleotide composition via the auto/cross-covariance approach. Rigorous jackknife tests show that its anticipated accuracy is quite high. For most experimental scientists' convenience, a user-friendly web-server for the predictor has been provided at http://www.jci-bioinfo.cn/iRNAm5C-PseDNC along with a step-by-step user guide, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. It has not escaped our notice that the approach presented here can also be used to deal with many other problems in genome analysis.

Keywords: RNA 5-methylcytosine sites; auto/cross-covariance; physical-chemical property matrix; pseudo dinucleotide composition; web-server.

Figure 1. Schematic drawing to show the m⁵C modification in RNA: an important post-transcriptional modification (PTCM) in RNA [4, 5]

During the modification process, a methyl group is attached to the 5th atom of the 6-atom ring. SAM and SAH are the abbreviations of S-adenosylmethionine and S-adenosylhomocysteine, respectively. The former is the source of the methyl group; while the latter, the byproduct.

Figure 2. A graphical illustration to show the proposed predictor's performances via the ROC (receiver operating characteristic) curves [29, 30]

The area under the ROC curve is called AUC (area under the curve). The greater the AUC value is, the better the performance will be. See the text for further explanation.