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Nucleic Acids Research Papers on Co-Expression, Variant Prioritization, MicroRNA Tools

A Cold Spring Harbor Laboratory team presents a free, online tool for tracking down sets of conserved genes and comparing networks of co-expressed genes in species with sufficient RNA sequence and gene annotation data available. The approach, known as CoCoCoNet, "allows users to access novel research areas by querying and comparing well-powered co-expression networks for 14 species," the researchers explain. For the study, the authors used CoCoCoNet to not only dig into co-expression modules involving more than 100 genes previously implicated in autism spectrum disorder, but also relied on the tool to consider highly co-expressed gene modules in the yeast model organism Saccharomyces cerevisiae in relation to networks of corresponding genes in zebrafish, fruit flies, and other species. "CoCoCoNet provides fast enrichment and conservation scores, displayed in a user-friendly manner," they write, adding that "future releases will encompass data from a wider variety of organisms as new research emerges."

Researchers in Germany outline a web resource for finding and prioritizing candidate and causal DNA variants in genetic studies of rare diseases with the help of population frequency, functional, pathogenicity scores, and other clues. The team describes the approach, known as VarFish, as a "user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics." The tool is aimed at analyzing variants in diagnostic and research contexts, the authors add, and includes support for more tailored laboratory information that can be shared between collaborating researchers. "Future development will focus on the extension of re-analysis features, cross-center collaboration," they write, "and supporting the analysis of structural variants, and support from whole genome data."

Finally, a team from France describes an online application designed for analyzing microRNA datasets with an eye to sharing related data and developing data-driven hypotheses related to miRNAs found through high-throughput analyses. The miRViz visualization and interpretation tool is currently applicable to miRNA datasets from 11 species, the researchers explain, and their proof-of-principle experiments point to the possibility of using the tool to focus on miRNAs and miRNA families relevant to various cancer types. "We propose that the web server application miRViz can be used to visualize numerical miRNA datasets," the researchers report, noting that "the network-based visualization proposed here provides clear ways to present datasets that are complementary to volcano plots for expression data."