SJARACNe: a scalable software tool for gene network reverse engineering from big data.

ABSTRACT:

Summary

Over the last two decades, we have observed an exponential increase in the number of generated array or sequencing-based transcriptomic profiles. Reverse engineering of biological networks from high-throughput gene expression profiles has been one of the grand challenges in systems biology. The Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) represents one of the most effective and widely-used tools to address this challenge. However, existing ARACNe implementations do not efficiently process big input data with thousands of samples. Here we present an improved implementation of the algorithm, SJARACNe, to solve this big data problem, based on sophisticated software engineering. The new scalable SJARACNe package achieves a dramatic improvement in com

SUBMITTER: Khatamian A 

PROVIDER: S-EPMC6581437 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature