Predicting disease-related genes by path structure and community structure in protein-protein networks
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Publication:3303203
DOI10.1088/1742-5468/AAE02BzbMATH Open1456.92087arXiv1707.06846OpenAlexW3100398599WikidataQ129034051 ScholiaQ129034051MaRDI QIDQ3303203FDOQ3303203
Authors: Ke Hu, Jingbo Hu, Liang Tang, Ju Xiang, Jinlong Ma, Yuanyuan Gao, Yan Zhang, Hui-Jia Li 
Publication date: 11 August 2020
Published in: Journal of Statistical Mechanics: Theory and Experiment (Search for Journal in Brave)
Abstract: Network-based computational approaches to predict unknown genes associated with certain diseases are of considerable significance for uncovering the molecular basis of human diseases. In this paper, we proposed a kind of new disease-gene-prediction methods by combining the path-based similarity with the community structure in the human protein-protein interaction network. Firstly, we introduced a set of path-based similarity indices, a novel community-based similarity index, and a new similarity combining the path-based similarity index. Then we assessed the statistical significance of the measures in distinguishing the disease genes from non-disease genes, to confirm their availability in predicting disease genes. Finally, we applied these measures to the disease-gene prediction of single disease-gene family, and analyzed the performance of these measures in disease-gene prediction, especially the effect of the community structure on the prediction performance in detail. The results indicated that genes associated with the same or similar diseases commonly reside in the same community of the protein-protein interaction network, and the community structure is greatly helpful for the disease-gene prediction.
Full work available at URL: https://arxiv.org/abs/1707.06846
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Cited In (15)
- Link prediction in protein-protein interaction network: a similarity multiplied similarity algorithm with paths of length three
- Network diffusion with centrality measures to identify disease-related genes
- An ensemble of random graphs with identical degree distribution
- A computational approach inspired by simulated annealing to study the stability of protein interaction networks in cancer and neurological disorders
- Topology association analysis in weighted protein interaction network for gene prioritization
- Community detection in disease-gene network based on principal component analysis
- Random growth networks with exponential degree distribution
- Graph centrality based prediction of cancer genes
- Identifying disease‐associated biomarker network features through conditional graphical model
- Logistic regression augmented community detection for network data with application in identifying autism-related gene pathways
- Integrating gene expression and protein interaction data for signaling pathway prediction of Alzheimer's disease
- Disease embryo development network reveals the relationship between disease genes and embryo development genes
- Preprocessing and analyzing genetic data with complex networks: an application to Obstructive Nephropathy
- A novel measure for finding disease-specific genes from the biomedical literature
- Using protein interactome similarity to improve \textit{random walk with restart model} for drug repurposing
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