scholarly journals BGRMI: A method for inferring gene regulatory networks from time-course gene expression data and its application in breast cancer research

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Luis F. Iglesias-Martinez ◽  
Walter Kolch ◽  
Tapesh Santra
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cancer Research ◽  
Gene Expression Data ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Time Course ◽  
Breast Cancer Research ◽  
Expression Data ◽  
Gene Regulatory

scholarly journals A big data pipeline: Identifying dynamic gene regulatory networks from time-course Gene Expression Omnibus data with applications to influenza infection

2018 ◽  
Vol 27 (7) ◽  
pp. 1930-1955 ◽  
Author(s):  
Michelle Carey ◽  
Juan Camilo Ramírez ◽  
Shuang Wu ◽  
Hulin Wu
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Gene Regulatory Networks ◽  
Host Response ◽  
Regulatory Networks ◽  
Time Course ◽  
Influenza Infection ◽  
Gene Expression Omnibus ◽  
Expression Data ◽  
Gene Regulatory

A biological host response to an external stimulus or intervention such as a disease or infection is a dynamic process, which is regulated by an intricate network of many genes and their products. Understanding the dynamics of this gene regulatory network allows us to infer the mechanisms involved in a host response to an external stimulus, and hence aids the discovery of biomarkers of phenotype and biological function. In this article, we propose a modeling/analysis pipeline for dynamic gene expression data, called Pipeline4DGEData, which consists of a series of statistical modeling techniques to construct dynamic gene regulatory networks from the large volumes of high-dimensional time-course gene expression data that are freely available in the Gene Expression Omnibus repository. This pipeline has a consistent and scalable structure that allows it to simultaneously analyze a large number of time-course gene expression data sets, and then integrate the results across different studies. We apply the proposed pipeline to influenza infection data from nine studies and demonstrate that interesting biological findings can be discovered with its implementation.

Inference of Gene Regulatory Networks by Topological Prior Information and Data Integration

Biotechnology ◽  
2019 ◽  
pp. 265-304
Author(s):  
David Correa Martins Jr. ◽  
Fabricio Martins Lopes ◽  
Shubhra Sankar Ray
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Prior Information ◽  
Heterogeneous Data ◽  
Data Sources ◽  
Expression Data ◽  
Heterogeneous Data Sources ◽  
Gene Regulatory

The inference of Gene Regulatory Networks (GRNs) is a very challenging problem which has attracted increasing attention since the development of high-throughput sequencing and gene expression measurement technologies. Many models and algorithms have been developed to identify GRNs using mainly gene expression profile as data source. As the gene expression data usually has limited number of samples and inherent noise, the integration of gene expression with several other sources of information can be vital for accurately inferring GRNs. For instance, some prior information about the overall topological structure of the GRN can guide inference techniques toward better results. In addition to gene expression data, recently biological information from heterogeneous data sources have been integrated by GRN inference methods as well. The objective of this chapter is to present an overview of GRN inference models and techniques with focus on incorporation of prior information such as, global and local topological features and integration of several heterogeneous data sources.

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