MaxLink: network-based prioritization of genes tightly linked to a disease seed set

Dimitri Guala; Erik Sjölund; Erik L L Sonnhammer

doi:10.1093/bioinformatics/btu344

MaxLink: network-based prioritization of genes tightly linked to a disease seed set

Bioinformatics. 2014 Sep 15;30(18):2689-90. doi: 10.1093/bioinformatics/btu344. Epub 2014 May 20.

Authors

Dimitri Guala¹, Erik Sjölund¹, Erik L L Sonnhammer²

Affiliations

¹ Stockholm Bioinformatics Centre, Science for Life Laboratory, SE-17121 Solna, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-11321, Sweden and Swedish eScience Research Center, SE-10450 Stockholm, Sweden Stockholm Bioinformatics Centre, Science for Life Laboratory, SE-17121 Solna, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-11321, Sweden and Swedish eScience Research Center, SE-10450 Stockholm, Sweden.
² Stockholm Bioinformatics Centre, Science for Life Laboratory, SE-17121 Solna, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-11321, Sweden and Swedish eScience Research Center, SE-10450 Stockholm, Sweden Stockholm Bioinformatics Centre, Science for Life Laboratory, SE-17121 Solna, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-11321, Sweden and Swedish eScience Research Center, SE-10450 Stockholm, Sweden Stockholm Bioinformatics Centre, Science for Life Laboratory, SE-17121 Solna, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-11321, Sweden and Swedish eScience Research Center, SE-10450 Stockholm, Sweden.

PMID: 24849579
DOI: 10.1093/bioinformatics/btu344

Abstract

MaxLink, a guilt-by-association network search algorithm, has been made available as a web resource and a stand-alone version. Based on a user-supplied list of query genes, MaxLink identifies and ranks genes that are tightly linked to the query list. This functionality can be used to predict potential disease genes from an initial set of genes with known association to a disease. The original algorithm, used to identify and rank novel genes potentially involved in cancer, has been updated to use a more statistically sound method for selection of candidate genes and made applicable to other areas than cancer. The algorithm has also been made faster by re-implementation in C++, and the Web site uses FunCoup 3.0 as the underlying network.

Availability and implementation: MaxLink is freely available at http://maxlink.sbc.su.se both as a web service and a stand-alone application for download.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Breast Neoplasms / genetics
Computational Biology / methods*
Disease / genetics*
Humans
Internet
Programming Languages
Software*