Probing lncRNA–Protein Interactions: Data Repositories, Models, and Algorithms

Abstract

Identifying lncRNA-protein interactions (LPIs) is vital to understanding various key biological processes. Wet experiments found a few LPIs, but experimental methods are costly and time-consuming. Therefore, computational methods are increasingly exploited to capture LPI candidates. We introduced relevant data repositories, focused on two types of LPI prediction models: network-based methods and machine learning-based methods. Machine learning-based methods contain matrix factorization-based techniques and ensemble learning-based techniques. To detect the performance of computational methods, we compared parts of LPI prediction models on Leave-One-Out cross-validation (LOOCV) and fivefold cross-validation. The results show that SFPEL-LPI obtained the best performance of AUC. Although computational models have efficiently unraveled some LPI candidates, there are many limitations involved. We discussed future directions to further boost LPI predictive performance.Keywords: lncRNA-protein interaction, computational method, network-based method, machine learning-based method, data repositories

RNMFMDA: A Microbe-Disease Association Identification Method Based on Reliable Negative Sample Selection and Logistic Matrix Factorization With Neighborhood Regularization

“…In the future, we will construct a multi-partite network by integrating MDAs, disease-gene associations (Tran et al, 2020), miRNA-disease associations (Peng et al, 2018a;Huang et al, 2019), long non-coding RNA-protein interactions (Zhao et al, 2018;Peng et al, 2019), and long non-coding RNA-disease associations (Chen et al, 2018;. More importantly, we will still develop more robust models, for example, ensemble strategy (Hu et al, 2018) and deep learning-based models (Min et al, 2017;Peng L. et al, 2018) to improve MDA prediction.…”

Downregulation of Long Non-coding RNA Nuclear Paraspeckle Assembly Transcript 1 Inhibits MEG-01 Differentiation and Platelet-Like Particles Activity

“…Further study is required. Long non-coding RNAs are a type of noncoding RNA, defined as being transcripts of more than 200 nucleotides in length, which cannot be translated into proteins (Peng et al, 2019). Excessive platelet activation is associated with an increased risk of thrombosis and there are few studies on the effects of lncRNAs on platelet activity (Zhou et al, 2019).…”

Decoding LncRNAs

“…For their detailed comparison we recommend the following article [ 160 ]. In addition, many tools focus on lncRNA–protein interaction, such as NPInter [ 169 , 170 ], starBase [ 171 ] and several others [ 172 ]. Additionally, RNA Interactome Repository-RNAInter is more comprehensive tool collecting information from published data along with another 35 database resources [ 173 ].…”