Gene prediction of aging-related diseases based on DNN and Mashup

• Published in: BMC bioinformatics Vol. 22; no. 1; p. 597
• Main Authors: Ye, Junhua, Wang, Shunfang, Yang, Xin, Tang, Xianjun
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 17.12.2021; BioMed Central; BMC
• Subjects: Age related diseases; Aging; Algorithms; Analysis; Artificial neural networks; Bioinformatics; Classifiers; Coders; Computational Biology; Datasets; Deep learning; Deep neural networks; Diseases; Encyclopedias; Gene expression; Gene Ontology; Gene prediction; Genes; Genetic aspects; Genomes; Health aspects; Hypothesis testing; Infectious diseases; Information sources; Learning algorithms; Machine learning; Mashup; Methods; Neural networks; Neural Networks, Computer; Ontology; Physiological aspects; Protein-protein interactions; Proteins; Protein–protein interaction; China; Gene ontology; Gene prediction; Deep neural networks; Mashup; Protein–protein interaction
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-021-04518-5

At present, the bioinformatics research on the relationship between aging-related diseases and genes is mainly through the establishment of a machine learning multi-label model to classify each gene. Most of the existing methods for predicting pathogenic genes mainly rely on specific types of gene features, or directly encode multiple features with different dimensions, use the same encoder to concatenate and predict the final results, which will be subject to many limitations in the applicability of the algorithm. Possible shortcomings of the above include: incomplete coverage of gene features by a single type of biomics data, overfitting of small dimensional datasets by a single encoder, or underfitting of larger dimensional datasets. We use the known gene disease association data and gene descriptors, such as gene ontology terms (GO), protein interaction data (PPI), PathDIP, Kyoto Encyclopedia of genes and genomes Genes (KEGG), etc, as input for deep learning to predict the association between genes and diseases. Our innovation is to use Mashup algorithm to reduce the dimensionality of PPI, GO and other large biological networks, and add new pathway data in KEGG database, and then combine a variety of biological information sources through modular Deep Neural Network (DNN) to predict the genes related to aging diseases. The results show that our algorithm is more effective than the standard neural network algorithm (the Area Under the ROC curve from 0.8795 to 0.9153), gradient enhanced tree classifier and logistic regression classifier. In this paper, we firstly use DNN to learn the similar genes associated with the known diseases from the complex multi-dimensional feature space, and then provide the evidence that the assumed genes are associated with a certain disease.