DiffGRN: differential gene regulatory network analysis

NetDiff – Bayesian model selection for differential gene regulatory network inference

Differential networks allow us to better understand the changes in cellular processes that are exhibited in conditions of interest, identifying variations in gene regulation or protein interaction between, for example, cases and controls, or in response to external stimuli. Here we present a novel methodology for the inference of differential gene regulatory networks from gene expression microa...

Identifying Gene Regulatory Network as Differential Equation by Genetic Programming

This paper proposes an evolutionary method of identifying the gene regulatory network represented as a differential equation system. As the technology in DNA micro arrays has developed, large quantities of gene’s expression data are becoming more available. As a result, it is essential to get information as to the gene regulatory network from the observed data of gene’s expression. Among many p...

Estimation of Gene Regulatory Network Using Stochastic Differential Equation Model

Identifying gene regulatory network rewiring using latent differential graphical models

Gene regulatory networks (GRNs) are highly dynamic among different tissue types. Identifying tissue-specific gene regulation is critically important to understand gene function in a particular cellular context. Graphical models have been used to estimate GRN from gene expression data to distinguish direct interactions from indirect associations. However, most existing methods estimate GRN for a...

Differential network analysis reveals dysfunctional regulatory networks in gastric carcinogenesis.

Gastric Carcinoma is one of the most common cancers in the world. A large number of differentially expressed genes have been identified as being associated with gastric cancer progression, however, little is known about the underlying regulatory mechanisms. To address this problem, we developed a differential networking approach that is characterized by including a nascent methodology, differen...