Dataset Information

Genome-wide prediction and prioritization of human aging genes by data fusion: a machine learning approach.

ABSTRACT: BACKGROUND:Machine learning can effectively nominate novel genes for various research purposes in the laboratory. On a genome-wide scale, we implemented multiple databases and algorithms to predict and prioritize the human aging genes (PPHAGE). RESULTS:We fused data from 11 databases, and used Naïve Bayes classifier and positive unlabeled learning (PUL) methods, NB, Spy, and Rocchio-SVM, to rank human genes in respect with their implication in aging. The PUL methods enabled us to identify a list of negative (non-aging) genes to use alongside the seed (known age-related) genes in the ranking process. Comparison of the PUL algorithms revealed that none of the methods for identifying a negative sample were advantageous over other methods, and their simultaneous use in a form of fusion was critical for obtaining optimal results (PPHAGE is publicly available at https://cbb.ut.ac.ir/pphage). CONCLUSION:We predict and prioritize over 3,000 candidate age-related genes in human, based on significant ranking scores. The identified candidate genes are associated with pathways, ontologies, and diseases that are linked to aging, such as cancer and diabetes. Our data offer a platform for future experimental research on the genetic and biological aspects of aging. Additionally, we demonstrate that fusion of PUL methods and data sources can be successfully used for aging and disease candidate gene prioritization.

SUBMITTER: Arabfard M

PROVIDER: S-EPMC6842548 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Genome-wide prediction and prioritization of human aging genes by data fusion: a machine learning approach.

Arabfard Masoud M Ohadi Mina M Rezaei Tabar Vahid V Delbari Ahmad A Kavousi Kaveh K

BMC genomics 20191109 1

<h4>Background</h4>Machine learning can effectively nominate novel genes for various research purposes in the laboratory. On a genome-wide scale, we implemented multiple databases and algorithms to predict and prioritize the human aging genes (PPHAGE).<h4>Results</h4>We fused data from 11 databases, and used Naïve Bayes classifier and positive unlabeled learning (PUL) methods, NB, Spy, and Rocchio-SVM, to rank human genes in respect with their implication in aging. The PUL methods enabled us to ...[more]

PMID: 31706268

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Project description:BACKGROUND: The genome-wide identification of both morbid genes, i.e., those genes whose mutations cause hereditary human diseases, and druggable genes, i.e., genes coding for proteins whose modulation by small molecules elicits phenotypic effects, requires experimental approaches that are time-consuming and laborious. Thus, a computational approach which could accurately predict such genes on a genome-wide scale would be invaluable for accelerating the pace of discovery of causal relationships between genes and diseases as well as the determination of druggability of gene products. RESULTS: In this paper we propose a machine learning-based computational approach to predict morbid and druggable genes on a genome-wide scale. For this purpose, we constructed a decision tree-based meta-classifier and trained it on datasets containing, for each morbid and druggable gene, network topological features, tissue expression profile and subcellular localization data as learning attributes. This meta-classifier correctly recovered 65% of known morbid genes with a precision of 66% and correctly recovered 78% of known druggable genes with a precision of 75%. It was than used to assign morbidity and druggability scores to genes not known to be morbid and druggable and we showed a good match between these scores and literature data. Finally, we generated decision trees by training the J48 algorithm on the morbidity and druggability datasets to discover cellular rules for morbidity and druggability and, among the rules, we found that the number of regulating transcription factors and plasma membrane localization are the most important factors to morbidity and druggability, respectively. CONCLUSIONS: We were able to demonstrate that network topological features along with tissue expression profile and subcellular localization can reliably predict human morbid and druggable genes on a genome-wide scale. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing morbidity and druggability.

Project description:BackgroundControlling the COVID-19 outbreak in Brazil is a challenge due to the population's size and urban density, inefficient maintenance of social distancing and testing strategies, and limited availability of testing resources.ObjectiveThe purpose of this study is to effectively prioritize patients who are symptomatic for testing to assist early COVID-19 detection in Brazil, addressing problems related to inefficient testing and control strategies.MethodsRaw data from 55,676 Brazilians were preprocessed, and the chi-square test was used to confirm the relevance of the following features: gender, health professional, fever, sore throat, dyspnea, olfactory disorders, cough, coryza, taste disorders, and headache. Classification models were implemented relying on preprocessed data sets; supervised learning; and the algorithms multilayer perceptron (MLP), gradient boosting machine (GBM), decision tree (DT), random forest (RF), extreme gradient boosting (XGBoost), k-nearest neighbors (KNN), support vector machine (SVM), and logistic regression (LR). The models' performances were analyzed using 10-fold cross-validation, classification metrics, and the Friedman and Nemenyi statistical tests. The permutation feature importance method was applied for ranking the features used by the classification models with the highest performances.ResultsGender, fever, and dyspnea were among the highest-ranked features used by the classification models. The comparative analysis presents MLP, GBM, DT, RF, XGBoost, and SVM as the highest performance models with similar results. KNN and LR were outperformed by the other algorithms. Applying the easy interpretability as an additional comparison criterion, the DT was considered the most suitable model.ConclusionsThe DT classification model can effectively (with a mean accuracy≥89.12%) assist COVID-19 test prioritization in Brazil. The model can be applied to recommend the prioritizing of a patient who is symptomatic for COVID-19 testing.

Dataset Information

Genome-wide prediction and prioritization of human aging genes by data fusion: a machine learning approach.

Publications

Genome-wide prediction and prioritization of human aging genes by data fusion: a machine learning approach.

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