Publications by authors named "Zi-Ang Shen"

4 Publications

  • Page 1 of 1

NPI-GNN: Predicting ncRNA-protein interactions with deep graph neural networks.

Brief Bioinform 2021 Apr 5. Epub 2021 Apr 5.

College of Intelligence and Computing, Tianjin University, Tianjin 300350, China.

Noncoding RNAs (ncRNAs) play crucial roles in many biological processes. Experimental methods for identifying ncRNA-protein interactions (NPIs) are always costly and time-consuming. Many computational approaches have been developed as alternative ways. In this work, we collected five benchmarking datasets for predicting NPIs. Based on these datasets, we evaluated and compared the prediction performances of existing machine-learning based methods. Graph neural network (GNN) is a recently developed deep learning algorithm for link predictions on complex networks, which has never been applied in predicting NPIs. We constructed a GNN-based method, which is called Noncoding RNA-Protein Interaction prediction using Graph Neural Networks (NPI-GNN), to predict NPIs. The NPI-GNN method achieved comparable performance with state-of-the-art methods in a 5-fold cross-validation. In addition, it is capable of predicting novel interactions based on network information and sequence information. We also found that insufficient sequence information does not affect the NPI-GNN prediction performance much, which makes NPI-GNN more robust than other methods. As far as we can tell, NPI-GNN is the first end-to-end GNN predictor for predicting NPIs. All benchmarking datasets in this work and all source codes of the NPI-GNN method have been deposited with documents in a GitHub repo (https://github.com/AshuiRUA/NPI-GNN).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bib/bbab051DOI Listing
April 2021

LPI-SKF: Predicting lncRNA-Protein Interactions Using Similarity Kernel Fusions.

Front Genet 2020 9;11:615144. Epub 2020 Dec 9.

College of Intelligence and Computing, Tianjin University, Tianjin, China.

Long non-coding RNAs (lncRNAs) play an important role in serval biological activities, including transcription, splicing, translation, and some other cellular regulation processes. lncRNAs perform their biological functions by interacting with various proteins. The studies on lncRNA-protein interactions are of great value to the understanding of lncRNA functional mechanisms. In this paper, we proposed a novel model to predict potential lncRNA-protein interactions using the SKF (similarity kernel fusion) and LapRLS (Laplacian regularized least squares) algorithms. We named this method the LPI-SKF. Various similarities of both lncRNAs and proteins were integrated into the LPI-SKF. LPI-SKF can be applied in predicting potential interactions involving novel proteins or lncRNAs. We obtained an AUROC (area under receiver operating curve) of 0.909 in a 5-fold cross-validation, which outperforms other state-of-the-art methods. A total of 19 out of the top 20 ranked interaction predictions were verified by existing data, which implied that the LPI-SKF had great potential in discovering unknown lncRNA-protein interactions accurately. All data and codes of this work can be downloaded from a GitHub repository (https://github.com/zyk2118216069/LPI-SKF).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2020.615144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758075PMC
December 2020

DPPN-SVM: Computational Identification of Mis-Localized Proteins in Cancers by Integrating Differential Gene Expressions With Dynamic Protein-Protein Interaction Networks.

Front Genet 2020 23;11:600454. Epub 2020 Oct 23.

College of Intelligence and Computing, Tianjin University, Tianjin, China.

Eukaryotic cells contain numerous components, which are known as subcellular compartments or subcellular organelles. Proteins must be sorted to proper subcellular compartments to carry out their molecular functions. Mis-localized proteins are related to various cancers. Identifying mis-localized proteins is important in understanding the pathology of cancers and in developing therapies. However, experimental methods, which are used to determine protein subcellular locations, are always costly and time-consuming. We tried to identify cancer-related mis-localized proteins in three different cancers using computational approaches. By integrating gene expression profiles and dynamic protein-protein interaction networks, we established DPPN-SVM (Dynamic Protein-Protein Network with Support Vector Machine), a predictive model using the SVM classifier with diffusion kernels. With this predictive model, we identified a number of mis-localized proteins. Since we introduced the dynamic protein-protein network, which has never been considered in existing works, our model is capable of identifying more mis-localized proteins than existing studies. As far as we know, this is the first study to incorporate dynamic protein-protein interaction network in identifying mis-localized proteins in cancers.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2020.600454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7644922PMC
October 2020

Predicting lncRNA-Protein Interactions With miRNAs as Mediators in a Heterogeneous Network Model.

Front Genet 2019 22;10:1341. Epub 2020 Jan 22.

College of Intelligence and Computing, Tianjin University, Tianjin, China.

Long non-coding RNAs (lncRNAs) play important roles in various biological processes, where lncRNA-protein interactions are usually involved. Therefore, identifying lncRNA-protein interactions is of great significance to understand the molecular functions of lncRNAs. Since the experiments to identify lncRNA-protein interactions are always costly and time consuming, computational methods are developed as alternative approaches. However, existing lncRNA-protein interaction predictors usually require prior knowledge of lncRNA-protein interactions with experimental evidences. Their performances are limited due to the number of known lncRNA-protein interactions. In this paper, we explored a novel way to predict lncRNA-protein interactions without direct prior knowledge. MiRNAs were picked up as mediators to estimate potential interactions between lncRNAs and proteins. By validating our results based on known lncRNA-protein interactions, our method achieved an AUROC (Area Under Receiver Operating Curve) of 0.821, which is comparable to the state-of-the-art methods. Moreover, our method achieved an improved AUROC of 0.852 by further expanding the training dataset. We believe that our method can be a useful supplement to the existing methods, as it provides an alternative way to estimate lncRNA-protein interactions in a heterogeneous network without direct prior knowledge. All data and codes of this work can be downloaded from GitHub (https://github.com/zyk2118216069/LncRNA-protein-interactions-prediction).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2019.01341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988623PMC
January 2020