相关实验视频

Updated: Sep 12, 2025

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

用未配对样本推断差异性基因调节网络推断的双倍最佳运输

Mengyu Li¹, Bencong Zhu², Cheng Meng³

¹Institute of Statistics and Big Data, Renmin University of China, Beijing 100872, China.

Bioinformatics (Oxford, England)

|August 4, 2025

概括

这项研究引入了双倍最佳传输 (OT),一种用于从未配对的基因表达数据中重建差异基因调节网络 (GRNs) 的新方法. 双重OT提供了卓越的效率和准确性,识别了胃癌中MET等关键调节基因.

科学领域:

计算生物学计算生物学
系统生物学系统生物学
生物信息学是一种生物信息学.

背景情况:

从基因表达数据中推断差异性基因调节网络 (GRNs) 具有挑战性,原因是可扩展性和准确性限制.
现有的方法往往需要配对样本,限制了比较GRN分析.

研究的目的:

开发一种高效准确的方法,从未配对的基因表达特征中重建差异性GRNs.
解决目前GRN推断方法在可扩展性和处理高维数据方面的局限性.

主要方法:

模拟基因调节作为一个分布运输问题,使用一种新的两级最佳运输 (OT) 框架,称为双 OT.
雇用部分OT用于未配对样本的样本水平对齐.
从对齐的样本中利用强大的OT进行基因级GRN推断.

主要成果:

与最先进的方法相比,双重OT在重建不同网络规模的差异GRN方面表现出更高的效率和有效性.
对胃癌数据集的应用确定了原瘤基因MET作为癌症GRN的中心节点.
在早期瘤发生过程中MET的确定的作用及其治疗潜力验证了该方法的实用性.

结论:

双重OT提供了一个有效的解决方案,用于使用未配对样本进行差异GRN推断.
该方法提高了对胃癌等疾病的调节机制的理解.
鉴定了MET的中心作用,突出了其在胃癌发展中的重要性,以及作为潜在的治疗点.

更多相关视频

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

相关概念视频

Regulated mRNA Transport

Regulated mRNA Transport

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for k_a Estimation

This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Nonlinear Pharmacokinetics: Role of Transporters

Nonlinear Pharmacokinetics: Role of Transporters

A drug's nonlinear kinetics can be influenced by a diverse range of transporter proteins that serve as crucial players in drug distribution. These transporters, found within cells, can enhance or reduce local drug concentrations by facilitating the influx or efflux of drugs. For instance, the expression of xenobiotic transporters can be influenced by factors such as age and gender, potentially impacting the linearity of drug response.
Polymorphisms occurring in drug transporters can alter...

Short-distance Transport of Resources

Short-distance Transport of Resources

Short-distance transport refers to transport that occurs over a distance of just 2-3 cells, crossing the plasma membrane in the process. Small uncharged molecules, such as oxygen, carbon dioxide, and water, can diffuse across the plasma membrane on their own. In contrast, ions and larger molecules require the assistance of transport proteins due to their charge or size. Transport across membranes also occurs within individual cells, playing a variety of essential roles for the plant as a whole.

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...