The knowledge of protein function is essential for the study of biological processes, the understanding of disease mechanism and the exploration of novel therapeutic target. Apart from experimental methods, a number of in-silico approaches have been developed and extensively used for protein function prediction. Among these approaches, BLAST predicts functions based on protein sequence similarity, and machine learning predicts functional families from protein sequences irrespective of their similarity, which complements BLAST and other methods in predicting diverse classes of proteins including distantly related proteins and homologous proteins of different functions. However, their identification accuracies and the false discovery rate have not yet been assessed so far, which greatly limits the usage of these prediction algorithms. Herein, a comprehensive comparison of the performances among four popular functional prediction algorithms (BLAST, SVM, PNN and KNN) was conducted. In particular, the performance of these algorithms were systematically assessed by four metrics (sensitivity, specificity, accuracy and Matthews correlation coefficient) based on the independent test datasets generated from 93 protein families defined by UniProtKB Keywords. Moreover, the false discovery rates of these algorithms were evaluated by scanning the genomes of four representative model species (homo sapiens, arabidopsis thaliana, saccharomyces cerevisiae and mycobacterium tuberculosis). As a result, the substantially higher sensitivity and stability of BLAST and SVM were observed compared with that of PNN and KNN. But the machine learning algorithms (PNN, KNN and SVM) were found capable of significantly reducing the false discovery rate (SVM < PNN ≈ KNN). In summary, this study comprehensively assessed the performance of four popular algorithms applied to protein function prediction, which could facilitate the selection of the most appropriate method in the related biomedical research.

Right ventricular remodeling and its function are closely related to the symptom severity and survival of hypoxia pulmonary hypertension, but molecular mechanisms of cardiomyocyte hypertrophy and myocardial injury remain unclear. It evaluated the cardiac function (by right cardiac catheterization to measure right ventricular systolic pressure and mean pulmonary artery pressure), myocardial tissue morphology（Haematoxylin and Eosin）, myocardial hypertrophy (Wheat Germ Agglutinin Staining), then RNA sequencing was applied to explore the mechanism, which results were verified by western blot in final. Hypoxia developed pulmonary hypertension, right ventricular diastolic and systolic functions were enhanced in rats, such as the mean pulmonary artery pressure, systolic pressure of pulmonary artery, the max pressure of right ventricular, the mean right ventricular pressure, and the heart rate was significantly higher than that in control. We found that Hif-1 signaling pathway and p38-MAPK signaling pathway have been activated by hypoxia, and cardiomyocyte apoptosis also aggravated in the right ventricular, which might be one cause of cardiomyocyte hypertrophy and myocardial injury, and targeted intervention might be one potential prevention for cardiomyocyte hypertrophy and myocardial injury induced by hypoxia.