Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks
<p>Abstract</p> <p>Background</p> <p>Cellular constituents such as proteins, DNA, and RNA form a complex web of interactions that regulate biochemical homeostasis and determine the dynamic cellular response to external stimuli. It follows that detailed understanding of...
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doaj-828e3435c14c4c8191d7d8f89e363bb62020-11-25T01:17:51ZengBMCBMC Research Notes1756-05002011-10-014146210.1186/1756-0500-4-462Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networksOuzounis Christos ADrozdov IgnatShah Ajay MTsoka Sophia<p>Abstract</p> <p>Background</p> <p>Cellular constituents such as proteins, DNA, and RNA form a complex web of interactions that regulate biochemical homeostasis and determine the dynamic cellular response to external stimuli. It follows that detailed understanding of these patterns is critical for the assessment of fundamental processes in cell biology and pathology. Representation and analysis of cellular constituents through network principles is a promising and popular analytical avenue towards a deeper understanding of molecular mechanisms in a system-wide context.</p> <p>Findings</p> <p>We present Functional Genomics Assistant (FUGA) - an extensible and portable <smcaps>MATLAB</smcaps> toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network clustering, and functional enrichment statistics. In contrast to conventional differential expression analysis of individual genes, FUGA offers a framework for the study of system-wide properties of biological networks and highlights putative molecular targets using concepts of systems biology.</p> <p>Conclusion</p> <p>FUGA offers a simple and customizable framework for network analysis in a variety of systems biology applications. It is freely available for individual or academic use at <url>http://code.google.com/p/fuga</url>.</p> http://www.biomedcentral.com/1756-0500/4/462 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ouzounis Christos A Drozdov Ignat Shah Ajay M Tsoka Sophia |
spellingShingle |
Ouzounis Christos A Drozdov Ignat Shah Ajay M Tsoka Sophia Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks BMC Research Notes |
author_facet |
Ouzounis Christos A Drozdov Ignat Shah Ajay M Tsoka Sophia |
author_sort |
Ouzounis Christos A |
title |
Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks |
title_short |
Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks |
title_full |
Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks |
title_fullStr |
Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks |
title_full_unstemmed |
Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks |
title_sort |
functional genomics assistant (fuga): a toolbox for the analysis of complex biological networks |
publisher |
BMC |
series |
BMC Research Notes |
issn |
1756-0500 |
publishDate |
2011-10-01 |
description |
<p>Abstract</p> <p>Background</p> <p>Cellular constituents such as proteins, DNA, and RNA form a complex web of interactions that regulate biochemical homeostasis and determine the dynamic cellular response to external stimuli. It follows that detailed understanding of these patterns is critical for the assessment of fundamental processes in cell biology and pathology. Representation and analysis of cellular constituents through network principles is a promising and popular analytical avenue towards a deeper understanding of molecular mechanisms in a system-wide context.</p> <p>Findings</p> <p>We present Functional Genomics Assistant (FUGA) - an extensible and portable <smcaps>MATLAB</smcaps> toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network clustering, and functional enrichment statistics. In contrast to conventional differential expression analysis of individual genes, FUGA offers a framework for the study of system-wide properties of biological networks and highlights putative molecular targets using concepts of systems biology.</p> <p>Conclusion</p> <p>FUGA offers a simple and customizable framework for network analysis in a variety of systems biology applications. It is freely available for individual or academic use at <url>http://code.google.com/p/fuga</url>.</p> |
url |
http://www.biomedcentral.com/1756-0500/4/462 |
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