相关实验视频

Updated: Jun 17, 2025

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Published on: July 30, 2011

用树状基因表达数据重建Caenorhabditis elegans的基因调节网络

Yida Wu¹, Da Zhou¹, Jie Hu¹

¹School of Mathematical Sciences, Xiamen University, Zengcuo'an West Road, Siming District, Xiamen 361000, China.

Briefings in bioinformatics

|August 12, 2024

概括

这项研究引入了一种新的贝叶斯方法,从树状数据中重建基因调节网络,提高生物见解的准确性. 该方法成功地确定了已知的基因关系,并检测了Caenorhabditis elegans.的谱系特异性调节差异.

科学领域:

系统生物学系统生物学
计算生物学计算生物学
发展生物学发展生物学

背景情况:

基因调节网络 (GRNs) 对于理解生物学和医学中的基因调节至关重要.
使用时间序列或单细胞RNA测序数据的现有方法往往缺乏细胞或时间分辨率.
时间缩短的共聚焦显微镜在Caenorhabditis elegans中产生树状基因表达数据,提供细胞和时间分辨率,但存在分析挑战.

研究的目的:

从具有挑战性的树状基因表达数据中推断基因调节网络,开发一个全面的框架和一种新的贝叶斯方法.
通过整合细胞和时间信息来解决现有方法的局限性.
准确地重建GRNs并探索特定细胞系中的基因调节关系.

主要方法:

提出了一种基于时间延迟的布尔网络的新贝叶斯方法.
预先选过程和马尔科夫链蒙特卡洛算法用于参数估计.
该方法使用模拟研究进行了验证,并应用于Caenorhabditis elegans的真实树状数据集.

主要成果:

拟议的方法在模拟中显示了与现有的布尔网络推理算法相比更高的性能.
成功重建了Caenorhabditis elegans的五个子树的基因调节网络,恢复了已知的基因调节关系.
在不同细胞系子树的调节关系中检测到异质性.
研究了与人类疾病相关的潜在基因调节关系.

结论:

开发的贝叶斯方法有效地从树状数据中重建基因调节网络,克服了以前方法的局限性.
这种方法为基因调节动态,血统特异性差异和潜在的疾病机制提供了宝贵的见解.
该研究提供了一个强大的计算工具来分析复杂的生物数据,源代码可用于更广泛的使用.

关键词:

贝叶斯统计学贝叶斯统计学布尔网络是一个布尔网络.数据整合数据集成.基因监管网络基因监管网络树状的基因表达数据.

更多相关视频

Application of RNAi and Heat-shock-induced Transcription Factor Expression to Reprogram Germ Cells to Neurons in C. elegans

Application of RNAi and Heat-shock-induced Transcription Factor Expression to Reprogram Germ Cells to Neurons in C. elegans

Published on: January 1, 2018

Quantification of Information Encoded by Gene Expression Levels During Lifespan Modulation Under Broad-range Dietary Restriction in C. elegans

Quantification of Information Encoded by Gene Expression Levels During Lifespan Modulation Under Broad-range Dietary Restriction in C. elegans

Published on: August 16, 2017

相关概念视频

Reporter Genes

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...