SysFinder: A customized platform for search, comparison and assisted design of appropriate animal models based on systematic similarity

Shuang Yang; Guoqing Zhang; Wan Liu; Zhen Wang; Jifeng Zhang; Dongshan Yang; Y. Eugene Chen; Hong Sun; Yixue Li

doi:10.1016/j.jgg.2017.05.001

Volume 44 Issue 5

May 2017

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Article Navigation > Journal of Genetics and Genomics > 2017 > 44(5): 251-258

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SysFinder: A customized platform for search, comparison and assisted design of appropriate animal models based on systematic similarity

doi: 10.1016/j.jgg.2017.05.001

Shuang Yang^{a, b, #},
Guoqing Zhang^{b, #},
Wan Liu^b,
Zhen Wang^c,
Jifeng Zhang^d,
Dongshan Yang^d,
Y. Eugene Chen^d,
Hong Sun^e,
Yixue Li^{a, b, c, f}

a
Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
b
Shanghai Center for Bioinformation Technology, Shanghai 200235, China
c
Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
d
Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
e
Biomedical Information Research Center, Children's Hospital of Shanghai, Shanghai 200040, China
f
Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China

More Information

Corresponding author: E-mail address: echenum@med.umich.edu (Y. Eugene Chen); E-mail address: sunhong@scbit.org (Hong Sun); E-mail address: yxli@sibs.ac.cn (Yixue Li)
Received Date: 2016-12-06
Accepted Date: 2017-05-03
Rev Recd Date: 2017-05-02

Available Online: 2017-05-04

Publish Date: 2017-05-20

Abstract

Abstract

Animal models are increasingly gaining values by cross-comparisons of response or resistance to clinical agents used for patients. However, many disease mechanisms and drug effects generated from animal models are not transferable to human. To address these issues, we developed SysFinder (http://lifecenter.sgst.cn/SysFinder), a platform for scientists to find appropriate animal models for translational research. SysFinder offers a “topic-centered” approach for systematic comparisons of human genes, whose functions are involved in a specific scientific topic, to the corresponding homologous genes of animal models. Scientific topic can be a certain disease, drug, gene function or biological pathway. SysFinder calculates multi-level similarity indexes to evaluate the similarities between human and animal models in specified scientific topics. Meanwhile, SysFinder offers species-specific information to investigate the differences in molecular mechanisms between humans and animal models. Furthermore, SysFinder provides a user-friendly platform for determination of short guide RNAs (sgRNAs) and homology arms to design a new animal model. Case studies illustrate the ability of SysFinder in helping experimental scientists. SysFinder is a useful platform for experimental scientists to carry out their research in the human molecular mechanisms.
- Database,
- Animal models,
- Function similarity

These authors contributed equally to this work.

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References(59)

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