You are here

Home

Regulatory Network

A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins. These play a central role in morphogenesis, the creation of body structures, which in turn is central to evolutionary developmental biology (evo-devo). [Source: Wikipedia]

Functional interpretation of microRNA-mRNA association

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The prediction of microRNA targets is a challenging task that has given rise to several prediction algorithms. Databases of predicted targets can be used in a microRNA target enrichment analysis, enhancing our capacity to extract functional information from gene lists. However, the available tools in this field analyze gene sets one by one limiting their use in a meta-analysis. Here, we present an R system for miRNA enrichment analysis that is suitable for systems biology.

Rating: 
Average: 5 (1 vote)

biRte

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

In the last years there has been an increasing effort to computationally model and predict the influence of regulators (transcription factors, miRNAs) on gene expression. Here we introduce biRte as a computationally attractive approach combining Bayesian inference of regulator activities with network reverse engineering. biRte integrates target gene predictions with different omics data entities (e.g. miRNA and mRNA data) into a joint probabilistic framework.

Rating: 
Average: 5 (1 vote)

Loregic

Submitted by ChenLiang on Thu, 04/06/2017 - 18:45

The topology of the gene-regulatory network has been extensively analyzed. Now, given the large amount of available functional genomic data, it is possible to go beyond this and systematically study regulatory circuits in terms of logic elements. To this end, we present Loregic, a computational method integrating gene expression and regulatory network data, to characterize the cooperativity of regulatory factors. Loregic uses all 16 possible two-input-one-output logic gates (e.g. AND or XOR) to describe triplets of two factors regulating a common target.

Rating: 
Average: 5 (1 vote)

Greglist

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The double helix is a conformation that genomic DNA usually assumes; under certain conditions, however, guanine-rich DNA sequences can form a four-stranded structure, G-quadruplex, which is found to play a role in regulating gene expression. Indeed, it has been demonstrated that the G-quadruplex formed in the c-MYC promoter suppresses its transcriptional activity. Recent studies suggest that G-quadruplex motifs (GQMs) are enriched in human gene promoters.

Rating: 
Average: 5 (1 vote)

DynaMod

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

A comprehensive analysis of enriched functional categories in differentially expressed genes is important to extract the underlying biological processes of genome-wide expression profiles. Moreover, identification of the network of significant functional modules in these dynamic processes is an interesting challenge. This study introduces DynaMod, a web-based application that identifies significant functional modules reflecting the change of modularity and differential expressions that are correlated with gene expression profiles under different conditions.

Rating: 
Average: 5 (1 vote)

Pages

Subscribe to Regulatory Network