Dataset Information

MiRNALoc: predicting miRNA subcellular localizations based on principal component scores of physico-chemical properties and pseudo compositions of di-nucleotides.

ABSTRACT: MicroRNAs (miRNAs) are one kind of non-coding RNA, play vital role in regulating several physiological and developmental processes. Subcellular localization of miRNAs and their abundance in the native cell are central for maintaining physiological homeostasis. Besides, RNA silencing activity of miRNAs is also influenced by their localization and stability. Thus, development of computational method for subcellular localization prediction of miRNAs is desired. In this work, we have proposed a computational method for predicting subcellular localizations of miRNAs based on principal component scores of thermodynamic, structural properties and pseudo compositions of di-nucleotides. Prediction accuracy was analyzed following fivefold cross validation, where?~?63-71% of AUC-ROC and?~?69-76% of AUC-PR were observed. While evaluated with independent test set, >?50% localizations were found to be correctly predicted. Besides, the developed computational model achieved higher accuracy than the existing methods. A user-friendly prediction server "miRNALoc" is freely accessible at https://cabgrid.res.in:8080/mirnaloc/ , by which the user can predict localizations of miRNAs.

SUBMITTER: Meher PK

PROVIDER: S-EPMC7471944 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Publications

miRNALoc: predicting miRNA subcellular localizations based on principal component scores of physico-chemical properties and pseudo compositions of di-nucleotides.

Meher Prabina Kumar PK Satpathy Subhrajit S Rao Atmakuri Ramakrishna AR

Scientific reports 20200903 1

MicroRNAs (miRNAs) are one kind of non-coding RNA, play vital role in regulating several physiological and developmental processes. Subcellular localization of miRNAs and their abundance in the native cell are central for maintaining physiological homeostasis. Besides, RNA silencing activity of miRNAs is also influenced by their localization and stability. Thus, development of computational method for subcellular localization prediction of miRNAs is desired. In this work, we have proposed a comp ...[more]

PMID: 32884018

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Project description:Computational methods have been widely used for the prediction of protein subcellular localization. However, these predictions are rarely validated experimentally and as a result remain questionable. Therefore, experimental validation of the predicted localizations is needed to assess the accuracy of predictions so that such methods can be confidently used to annotate the proteins of unknown localization. Previously, we published a method called ngLOC that predicts the localization of proteins targeted to ten different subcellular organelles. In this short report, we describe the accuracy of these predictions using experimental validations.We have experimentally validated the predicted subcellular localizations of 114 human proteins corresponding to nine different organelles in normal breast and breast cancer cell lines using live cell imaging/confocal microscopy. Target genes were cloned into expression vectors as GFP fusions and cotransfected with RFP-tagged organelle-specific gene marker into normal breast epithelial and breast cancer cell lines. Subcellular localization of each target protein is confirmed by colocalization with a co-expressed organelle-specific protein marker. Our results showed that about 82.5% of the predicted subcellular localizations coincided with the experimentally validated localizations. The highest agreement was found in the endoplasmic reticulum proteins, while the cytoplasmic location showed the least concordance. With the exclusion of cytoplasmic location, the average prediction accuracy increased to 90.4%. In addition, there was no difference observed in the protein subcellular localization between normal and cancer breast cell lines.The experimentally validated accuracy of ngLOC method with (82.5%) or without cytoplasmic location (90.4%) nears the prediction accuracy of 89%. These results demonstrate that the ngLOC method can be very useful for large-scale annotation of the unknown subcellular localization of proteins.

Dataset Information

MiRNALoc: predicting miRNA subcellular localizations based on principal component scores of physico-chemical properties and pseudo compositions of di-nucleotides.

Publications

miRNALoc: predicting miRNA subcellular localizations based on principal component scores of physico-chemical properties and pseudo compositions of di-nucleotides.

Similar Datasets

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