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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Autor*in:	Ouzounis Christos A [verfasserIn] Drozdov Ignat [verfasserIn] Shah Ajay M [verfasserIn] Tsoka Sophia [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2011

Übergeordnetes Werk:	In: BMC Research Notes - BMC, 2008, 4(2011), 1, p 462
Übergeordnetes Werk:	volume:4 ; year:2011 ; number:1, p 462

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/1756-0500-4-462

Katalog-ID:	DOAJ063276089

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allfields	10.1186/1756-0500-4-462 doi (DE-627)DOAJ063276089 (DE-599)DOAJ828e3435c14c4c8191d7d8f89e363bb6 DE-627 ger DE-627 rakwb eng QH301-705.5 Q1-390 Ouzounis Christos A verfasserin aut Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <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< Medicine R Biology (General) Science (General) Drozdov Ignat verfasserin aut Shah Ajay M verfasserin aut Tsoka Sophia verfasserin aut In BMC Research Notes BMC, 2008 4(2011), 1, p 462 (DE-627)559431805 (DE-600)2413336-X 17560500 nnns volume:4 year:2011 number:1, p 462 https://doi.org/10.1186/1756-0500-4-462 kostenfrei https://doaj.org/article/828e3435c14c4c8191d7d8f89e363bb6 kostenfrei http://www.biomedcentral.com/1756-0500/4/462 kostenfrei https://doaj.org/toc/1756-0500 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 4 2011 1, p 462
spelling	10.1186/1756-0500-4-462 doi (DE-627)DOAJ063276089 (DE-599)DOAJ828e3435c14c4c8191d7d8f89e363bb6 DE-627 ger DE-627 rakwb eng QH301-705.5 Q1-390 Ouzounis Christos A verfasserin aut Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <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< Medicine R Biology (General) Science (General) Drozdov Ignat verfasserin aut Shah Ajay M verfasserin aut Tsoka Sophia verfasserin aut In BMC Research Notes BMC, 2008 4(2011), 1, p 462 (DE-627)559431805 (DE-600)2413336-X 17560500 nnns volume:4 year:2011 number:1, p 462 https://doi.org/10.1186/1756-0500-4-462 kostenfrei https://doaj.org/article/828e3435c14c4c8191d7d8f89e363bb6 kostenfrei http://www.biomedcentral.com/1756-0500/4/462 kostenfrei https://doaj.org/toc/1756-0500 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 4 2011 1, p 462
allfields_unstemmed	10.1186/1756-0500-4-462 doi (DE-627)DOAJ063276089 (DE-599)DOAJ828e3435c14c4c8191d7d8f89e363bb6 DE-627 ger DE-627 rakwb eng QH301-705.5 Q1-390 Ouzounis Christos A verfasserin aut Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <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< Medicine R Biology (General) Science (General) Drozdov Ignat verfasserin aut Shah Ajay M verfasserin aut Tsoka Sophia verfasserin aut In BMC Research Notes BMC, 2008 4(2011), 1, p 462 (DE-627)559431805 (DE-600)2413336-X 17560500 nnns volume:4 year:2011 number:1, p 462 https://doi.org/10.1186/1756-0500-4-462 kostenfrei https://doaj.org/article/828e3435c14c4c8191d7d8f89e363bb6 kostenfrei http://www.biomedcentral.com/1756-0500/4/462 kostenfrei https://doaj.org/toc/1756-0500 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 4 2011 1, p 462
allfieldsGer	10.1186/1756-0500-4-462 doi (DE-627)DOAJ063276089 (DE-599)DOAJ828e3435c14c4c8191d7d8f89e363bb6 DE-627 ger DE-627 rakwb eng QH301-705.5 Q1-390 Ouzounis Christos A verfasserin aut Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <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< Medicine R Biology (General) Science (General) Drozdov Ignat verfasserin aut Shah Ajay M verfasserin aut Tsoka Sophia verfasserin aut In BMC Research Notes BMC, 2008 4(2011), 1, p 462 (DE-627)559431805 (DE-600)2413336-X 17560500 nnns volume:4 year:2011 number:1, p 462 https://doi.org/10.1186/1756-0500-4-462 kostenfrei https://doaj.org/article/828e3435c14c4c8191d7d8f89e363bb6 kostenfrei http://www.biomedcentral.com/1756-0500/4/462 kostenfrei https://doaj.org/toc/1756-0500 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 4 2011 1, p 462
allfieldsSound	10.1186/1756-0500-4-462 doi (DE-627)DOAJ063276089 (DE-599)DOAJ828e3435c14c4c8191d7d8f89e363bb6 DE-627 ger DE-627 rakwb eng QH301-705.5 Q1-390 Ouzounis Christos A verfasserin aut Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <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< Medicine R Biology (General) Science (General) Drozdov Ignat verfasserin aut Shah Ajay M verfasserin aut Tsoka Sophia verfasserin aut In BMC Research Notes BMC, 2008 4(2011), 1, p 462 (DE-627)559431805 (DE-600)2413336-X 17560500 nnns volume:4 year:2011 number:1, p 462 https://doi.org/10.1186/1756-0500-4-462 kostenfrei https://doaj.org/article/828e3435c14c4c8191d7d8f89e363bb6 kostenfrei http://www.biomedcentral.com/1756-0500/4/462 kostenfrei https://doaj.org/toc/1756-0500 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 4 2011 1, p 462
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title	Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks
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title_auth	Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks
abstract	<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<
abstractGer	<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<
abstract_unstemmed	<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<
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title_short	Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks
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