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Journal of Zhejiang University SCIENCE B

ISSN 1673-1581(Print), 1862-1783(Online), Monthly

Gene locations may contribute to predicting gene regulatory relationships

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.

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

Chinese Summary  <26> 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.

关键词组: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


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DOI:

10.1631/jzus.B1700303

CLC number:

TP181

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On-line Access:

2024-08-27

Received:

2023-10-17

Revision Accepted:

2024-05-08

Crosschecked:

2017-12-15

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