mLoc-mRNA: predicting multiple sub-cellular localization of mRNAs using random forest algorithm coupled with feature selection via elastic net

• Published in: BMC bioinformatics 2021-06, Vol.22 (1), p.1-342, Article 342
• Main Authors: Meher, Prabina Kumar, Rai, Anil, Rao, Atmakuri Ramakrishna
• Format: Article
• Language: English
• Subjects: Accuracy; Algorithms; Analysis; Bioinformatics; Cell division; Computational biology; Computer applications; Cytoplasm; Cytosol; Datasets; Endoplasmic reticulum; Feature selection; Gene expression; Gene sequencing; Hybridization; Localization; Machine learning; Mathematical models; Messenger RNA; Methodology; Methods; Microscopy; Physiological aspects; Predictions; Proteins; RNA sequencing; Software; Statistical analysis; Statistical models; Sub-cellular localization
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-021-04264-8

Localization of messenger RNAs (mRNAs) plays a crucial role in the growth and development of cells. Particularly, it plays a major role in regulating spatio-temporal gene expression. The in situ hybridization is a promising experimental technique used to determine the localization of mRNAs but it is costly and laborious. It is also a known fact that a single mRNA can be present in more than one location, whereas the existing computational tools are capable of predicting only a single location for such mRNAs. Thus, the development of high-end computational tool is required for reliable and timely prediction of multiple subcellular locations of mRNAs. Hence, we develop the present computational model to predict the multiple localizations of mRNAs. The mRNA sequences from 9 different localizations were considered. Each sequence was first transformed to a numeric feature vector of size 5460, based on the k-mer features of sizes 1-6. Out of 5460 k-mer features, 1812 important features were selected by the Elastic Net statistical model. The Random Forest supervised learning algorithm was then employed for predicting the localizations with the selected features. Five-fold cross-validation accuracies of 70.87, 68.32, 68.36, 68.79, 96.46, 73.44, 70.94, 97.42 and 71.77% were obtained for the cytoplasm, cytosol, endoplasmic reticulum, exosome, mitochondrion, nucleus, pseudopodium, posterior and ribosome respectively. With an independent test set, accuracies of 65.33, 73.37, 75.86, 72.99, 94.26, 70.91, 65.53, 93.60 and 73.45% were obtained for the respective localizations. The developed approach also achieved higher accuracies than the existing localization prediction tools. This study presents a novel computational tool for predicting the multiple localization of mRNAs. Based on the proposed approach, an online prediction server "mLoc-mRNA" is accessible at http://cabgrid.res.in:8080/mlocmrna/. The developed approach is believed to supplement the existing tools and techniques for the localization prediction of mRNAs.