UCL Discovery
UCL home » Library Services » Electronic resources » UCL Discovery

Using large-scale perturbations in gene network reconstruction

MacCarthy, T; Pomiankowski, A; Seymour, R; (2005) Using large-scale perturbations in gene network reconstruction. BMC BIOINFORMATICS , 6 , Article 11. 10.1186/1471-2105-6-11. Green open access

[thumbnail of 1471-2105-6-11.pdf]
Preview
PDF
1471-2105-6-11.pdf

Download (415kB)

Abstract

Background: Recent analysis of the yeast gene network shows that most genes have few inputs, indicating that enumerative gene reconstruction methods are both useful and computationally feasible. A simple enumerative reconstruction method based on a discrete dynamical system model is used to study how microarray experiments involving modulated global perturbations can be designed to obtain reasonably accurate reconstructions. The method is tested on artificial gene networks with biologically realistic in/out degree characteristics.Results: It was found that a relatively small number of perturbations significantly improve inference accuracy, particularly for low-order inputs of one or two genes. The perturbations themselves should alter the expression level of approximately 50-60% of the genes in the network.Conclusions: Time-series obtained from perturbations are a common form of expression data. This study illustrates how gene networks can be significantly reconstructed from such time-series while requiring only a relatively small number of calibrated perturbations, even for large networks, thus reducing experimental costs.

Type: Article
Title: Using large-scale perturbations in gene network reconstruction
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/1471-2105-6-11
Publisher version: http://www.ncbi.nlm.nih.gov/pmc/ articles/PMC54812...
Keywords: CELL-CYCLE, SACCHAROMYCES-CEREVISIAE
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
URI: https://discovery.ucl.ac.uk/id/eprint/512
Downloads since deposit
157Downloads
Download activity - last month
Download activity - last 12 months
Downloads by country - last 12 months

Archive Staff Only

View Item View Item