A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model.

Journal: Communications biology
Published Date: Sep 10, 2020

Abstract

The analyses of multi-omics data have revealed candidate genes for objective traits. However, they are integrated poorly, especially in non-model organisms, and they pose a great challenge for prioritizing candidate genes for follow-up experimental verification. Here, we present a general convolutional neural network model that integrates multi-omics information to prioritize the candidate genes of objective traits. By applying this model to Sus scrofa, which is a non-model organism, but one of the most important livestock animals, the model precision was 72.9%, recall 73.5%, and F1-Measure 73.4%, demonstrating a good prediction performance compared with previous studies in Arabidopsis thaliana and Oryza sativa. Additionally, to facilitate the use of the model, we present ISwine ( http://iswine.iomics.pro/ ), which is an online comprehensive knowledgebase in which we incorporated almost all the published swine multi-omics data. Overall, the results suggest that the deep learning strategy will greatly facilitate analyses of multi-omics integration in the future.

Authors

  • Yuhua Fu
    Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China.
  • Jingya Xu
    Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China.
  • Zhenshuang Tang
    Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China.
  • Lu Wang
    Department of Laboratory, Akesu Center of Disease Control and Prevention, Akesu, China.
  • Dong Yin
    Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China.
  • Yu Fan
    Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA. YFan1@mdanderson.org.
  • Dongdong Zhang
    Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea.
  • Fei Deng
  • Yanping Zhang
    Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, ‡School of Computer Science and Technology, and §Center of Information Support & Assurance Technology, Anhui University , Hefei, 230601 Anhui, China.
  • Haohao Zhang
    School of Computer Science and Technology, Wuhan University of Technology, Wuhan, 430070, China.
  • Haiyan Wang
    College of Chemistry and Material Science, Shandong Agricultural University, Tai'an 271018, PR China.
  • Wenhui Xing
  • Lilin Yin
    Northeastern University, Department of Chemistry, CHINA.
  • Shilin Zhu
    Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China.
  • Mengjin Zhu
    Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China.
  • Mei Yu
  • Xinyun Li
    Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China. xyli@mail.hzau.edu.cn.
  • Xiaolei Liu
    Department of Neurology, the First Affiliated Hospital of Kunming Medical University, Wuhua District, Kunming, Yunnan Province, China.
  • Xiaohui Yuan
  • Shuhong Zhao
    Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.

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