Full Text:   <304>

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CLC number: TP181

On-line Access: 2018-01-11

Received: 2017-06-08

Revision Accepted: 2017-11-19

Crosschecked: 2017-12-15

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Journal of Zhejiang University SCIENCE B 2018 Vol.19 No.1 P.25-37

10.1631/jzus.B1700303


Gene locations may contribute to predicting gene regulatory relationships


Author(s):  Jun Meng, Wen-Yuan Xu, Xiao Chen, Tao Lin, Xiao-Yu Deng

Affiliation(s):  Department of System Science and Engineering, School of Electrical Engineering, Zhejiang University, Hangzhou 310027, China; more

Corresponding email(s):   junmeng@zju.edu.cn

Key Words:  Prediction, Gene regulatory relationships, Order of gene location, Spatio-temporal neighborhood method, Zebrafish cardiogenesis


Jun Meng, Wen-Yuan Xu, Xiao Chen, Tao Lin, Xiao-Yu Deng. Gene locations may contribute to predicting gene regulatory relationships[J]. Journal of Zhejiang University Science B, 2018, 19(1): 25-37.

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doi="10.1631/jzus.B1700303"
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%T Gene locations may contribute to predicting gene regulatory relationships
%A Jun Meng
%A Wen-Yuan Xu
%A Xiao Chen
%A Tao Lin
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%DOI 10.1631/jzus.B1700303

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T1 - Gene locations may contribute to predicting gene regulatory relationships
A1 - Jun Meng
A1 - Wen-Yuan Xu
A1 - Xiao Chen
A1 - Tao Lin
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PB - Zhejiang University Press & Springer
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DOI - 10.1631/jzus.B1700303


Abstract: 
We propose that locations of genes on chromosomes can contribute to the prediction of gene regulatory relationships. We constructed a time-based gene regulatory network of zebrafish cardiogenesis on the basis of a spatio-temporal neighborhood method. Through the network, specific regulatory pathways and order of gene expression during zebrafish cardiogenesis were obtained. By comparing the order with locations of these genes on chromosomes, we discovered that there exists a reversal phenomenon between the order and order of gene locations. The discovery provides an inherent rule to instruct exploration of gene regulatory relationships. Specifically, the discovery can help to predict if regulatory relationships between genes exist and contribute to evaluating the correctness of discovered gene regulatory relationships.

基因位置可以用于预测基因调控关系

目的:证明基因位置顺序与基因调控顺序的关系,说明利用基因位置顺序信息可以作为预测基因调控关系的先验知识.
创新点:通过研究与斑马鱼心脏发育阶段有关的基因和miRNA,利用时空邻域法,建立了一个基于时间的基因调控网络.通过这个基因调控网络,我们获得了一些特殊的基因调控通路和基因之间调控的时间顺序.通过研究斑马鱼心脏发育阶段有关的基因在染色体上的位置,将基因位置顺序与基因调控时间顺序比较,我们发现了这两个顺序具有逆转现象.这个逆转现象的存在,可以帮助我们利用基因位置顺序来预测基因调控关系和调控的时间顺序.
方法:采用时空邻域法研究了斑马鱼心脏发育阶段的基因和miRNA,建立基因调控网络(图5),并通过进一步比较,得到了基因位置顺序和基因调控时间顺序的联系.
结论:基因位置顺序信息可以用于预测基因调控关系.

关键词:预测;基因调控关系;基因位置顺序信息;时空邻域法;斑马鱼心脏发育期

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

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