scholarly journals Network Inference from Gene Expression Data with Distance Correlation and Network Topology Centrality

Algorithms ◽  
2021 ◽  
Vol 14 (2) ◽  
pp. 61
Author(s):  
Kuan Liu ◽  
Haiyuan Liu ◽  
Dongyan Sun ◽  
Lei Zhang
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Gene Regulatory Networks ◽  
Network Topology ◽  
Regulatory Networks ◽  
Network Inference ◽  
Expression Data ◽  
Distance Correlation ◽  
Non Linear ◽  
Gene Regulatory

The reconstruction of gene regulatory networks based on gene expression data can effectively uncover regulatory relationships between genes and provide a deeper understanding of biological control processes. Non-linear dependence is a common problem in the regulatory mechanisms of gene regulatory networks. Various methods based on information theory have been developed to infer networks. However, the methods have introduced many redundant regulatory relationships in the network inference process. A recent measurement method called distance correlation has, in many cases, shown strong and computationally efficient non-linear correlations. In this paper, we propose a novel regulatory network inference method called the distance-correlation and network topology centrality network (DCNTC) method. The method is based on and extends the Local Density Measurement of Network Node Centrality (LDCNET) algorithm, which has the same choice of network centrality ranking as the LDCNET algorithm, but uses a simpler and more efficient distance correlation measure of association between genes. In this work, we integrate distance correlation and network topological centrality into the reasoning about the structure of gene regulatory networks. We will select optimal thresholds based on the characteristics of the distribution of each gene pair in relation to distance correlation. Experiments were carried out on four network datasets and their performance was compared.

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.

scholarly journals Chip-seq and gene expression data for the identification of functional sub-pathways: a proof of concept in lung cancer

2020 ◽  
Author(s):  
Xanthoula Atsalaki ◽  
Lefteris Koumakis ◽  
George Potamias ◽  
Manolis Tsiknakis
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Systems Biology ◽  
Gene Expression Data ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Integrative Approach ◽  
Expression Data ◽  
Gene Regulatory

AbstractHigh-throughput technologies, such as chromatin immunoprecipitation (ChIP) with massively parallel sequencing (ChIP-seq) have enabled cost and time efficient generation of immense amount of genome data. The advent of advanced sequencing techniques allowed biologists and bioinformaticians to investigate biological aspects of cell function and understand or reveal unexplored disease etiologies. Systems biology attempts to formulate the molecular mechanisms in mathematical models and one of the most important areas is the gene regulatory networks (GRNs), a collection of DNA segments that somehow interact with each other. GRNs incorporate valuable information about molecular targets that can be corellated to specific phenotype.In our study we highlight the need to develop new explorative tools and approaches for the integration of different types of -omics data such as ChIP-seq and GRNs using pathway analysis methodologies. We present an integrative approach for ChIP-seq and gene expression data on GRNs. Using public microarray expression samples for lung cancer and healthy subjects along with the KEGG human gene regulatory networks, we identified ways to disrupt functional sub-pathways on lung cancer with the aid of CTCF ChIP-seq data, as a proof of concept.We expect that such a systems biology pipeline could assist researchers to identify corellations and causality of transcription factors over functional or disrupted biological sub-pathways.

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