Jump to main content
Jump to site search

Issue 7, 2017
Previous Article Next Article

GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties

Author affiliations

Abstract

A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method. We present GeneSPIDER – a Matlab package for tuning, running, and evaluating inference algorithms that allows independent control of network and data properties to enable data-driven benchmarking. GeneSPIDER is uniquely suited to address this question by first extracting salient properties from the experimental data and then generating simulated networks and data that closely match these properties. It enables data-driven algorithm selection, estimation of inference accuracy from biological data, and a more multifaceted benchmarking. Included are generic pipelines for the design of perturbation experiments, bootstrapping, analysis of linear dependence, sample selection, scaling of SNR, and performance evaluation. With GeneSPIDER we aim to move the goal of network inference benchmarks from simple performance measurement to a deeper understanding of how the accuracy of an algorithm is determined by different combinations of network and data properties.

Graphical abstract: GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties

Back to tab navigation

Supplementary files

Publication details

The article was received on 25 Jan 2017, accepted on 20 Apr 2017 and first published on 25 Apr 2017


Article type: Paper
DOI: 10.1039/C7MB00058H
Citation: Mol. BioSyst., 2017,13, 1304-1312
  •   Request permissions

    GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties

    A. Tjärnberg, D. C. Morgan, M. Studham, T. E. M. Nordling and E. L. L. Sonnhammer, Mol. BioSyst., 2017, 13, 1304
    DOI: 10.1039/C7MB00058H

Search articles by author

Spotlight

Advertisements