Mahiar Mahjoub1,2,3, Daphne Ezer2,4,5. 1. Department of Mathematics, University of Cambridge, Cambridge CB3 0WA, UK. 2. The Alan Turing Institute, London NW1 2DB, UK. 3. Royal Prince Alfred Hospital, Central Clinical School, University of Sydney, Sydney, NSW 2050, Australia. 4. Department of Statistics, University of Warwick, Coventry CV4 7AL, UK. 5. Department of Biology, University of York, York, YO10 5NG, UK.
Abstract
MOTIVATION: Large gene networks can be dense and difficult to interpret in a biologically meaningful way. RESULTS: Here, we introduce PAFway, which estimates pairwise associations between functional annotations in biological networks and pathways. It answers the biological question: do genes that have a specific function tend to regulate genes that have a different specific function? The results can be visualized as a heatmap or a network of biological functions. We apply this package to reveal associations between functional annotations in an Arabidopsis thaliana gene network. AVAILABILITY AND IMPLEMENTATION: PAFway is submitted to CRAN. Currently available here: https://github.com/ezer/PAFway. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Large gene networks can be dense and difficult to interpret in a biologically meaningful way. RESULTS: Here, we introduce PAFway, which estimates pairwise associations between functional annotations in biological networks and pathways. It answers the biological question: do genes that have a specific function tend to regulate genes that have a different specific function? The results can be visualized as a heatmap or a network of biological functions. We apply this package to reveal associations between functional annotations in an Arabidopsis thaliana gene network. AVAILABILITY AND IMPLEMENTATION: PAFway is submitted to CRAN. Currently available here: https://github.com/ezer/PAFway. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Andreas Schlicker; Francisco S Domingues; Jörg Rahnenführer; Thomas Lengauer Journal: BMC Bioinformatics Date: 2006-06-15 Impact factor: 3.169