Modular network construction using eQTL data: an analysis of computational costs and benefits
Background: In this paper, we consider analytic methods for the integrated analysis of genomic DNA variation and mRNA expression (also named as eQTL data), to discover genetic networks that are associated with a complex trait of interest. Our focus is the systematic evaluation of the trade-off betw...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2014-02-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00040/full |
| _version_ | 1819074221871988736 |
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| author | Yen-Yi eHo Leslie Michael Cope Giovanni eParmigiani |
| author_facet | Yen-Yi eHo Leslie Michael Cope Giovanni eParmigiani |
| author_sort | Yen-Yi eHo |
| collection | DOAJ |
| description | Background: In this paper, we consider analytic methods for the integrated analysis of genomic DNA variation and mRNA expression (also named as eQTL data), to discover genetic networks that are associated with a complex trait of interest. Our focus is the systematic evaluation of the trade-off between network size and network search efficiency in the construction of these networks. <br/>Results: We developed a modular approach to network construction, building from smaller networks to larger ones, thereby reducing the search space while including more variables in the analysis. The goal is achieving a lower computational cost while maintaining high confidence in the resulting networks. As demonstrated in our simulation results, networks built in this way have low node/edge false discovery rate (FDR) and high node/edge sensitivity comparing to greedy search. We further demonstrate our method in a data set of cellular responses to two chemotherapeutic agents: docetaxel and 5-fluorouracil (5-FU), and identify biologically plausible networks that might describe resistances to these drugs.<br/>Conclusions: In this study, we suggest that guided comprehensive searches for parsimonious networks should be considered as an alternative to greedy network searches.<br/><br/> |
| first_indexed | 2024-12-21T18:06:05Z |
| format | Article |
| id | doaj.art-c3a26d1f6630478a94512373b3afe828 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-21T18:06:05Z |
| publishDate | 2014-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-c3a26d1f6630478a94512373b3afe8282022-12-21T18:54:56ZengFrontiers Media S.A.Frontiers in Genetics1664-80212014-02-01510.3389/fgene.2014.0004055546Modular network construction using eQTL data: an analysis of computational costs and benefitsYen-Yi eHo0Leslie Michael Cope1Giovanni eParmigiani2University of MinnesotaThe Sidney Kimmel Cancer Center, Johns Hopkins School of MedicineDana-Farber Cancer Institute and Harvard School of Public HealthBackground: In this paper, we consider analytic methods for the integrated analysis of genomic DNA variation and mRNA expression (also named as eQTL data), to discover genetic networks that are associated with a complex trait of interest. Our focus is the systematic evaluation of the trade-off between network size and network search efficiency in the construction of these networks. <br/>Results: We developed a modular approach to network construction, building from smaller networks to larger ones, thereby reducing the search space while including more variables in the analysis. The goal is achieving a lower computational cost while maintaining high confidence in the resulting networks. As demonstrated in our simulation results, networks built in this way have low node/edge false discovery rate (FDR) and high node/edge sensitivity comparing to greedy search. We further demonstrate our method in a data set of cellular responses to two chemotherapeutic agents: docetaxel and 5-fluorouracil (5-FU), and identify biologically plausible networks that might describe resistances to these drugs.<br/>Conclusions: In this study, we suggest that guided comprehensive searches for parsimonious networks should be considered as an alternative to greedy network searches.<br/><br/>http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00040/fulleQTLbayesian networkschemotherapy resistanceSearch algorithmNetwork variable selectionGenetic data integration |
| spellingShingle | Yen-Yi eHo Leslie Michael Cope Giovanni eParmigiani Modular network construction using eQTL data: an analysis of computational costs and benefits Frontiers in Genetics eQTL bayesian networks chemotherapy resistance Search algorithm Network variable selection Genetic data integration |
| title | Modular network construction using eQTL data: an analysis of computational costs and benefits |
| title_full | Modular network construction using eQTL data: an analysis of computational costs and benefits |
| title_fullStr | Modular network construction using eQTL data: an analysis of computational costs and benefits |
| title_full_unstemmed | Modular network construction using eQTL data: an analysis of computational costs and benefits |
| title_short | Modular network construction using eQTL data: an analysis of computational costs and benefits |
| title_sort | modular network construction using eqtl data an analysis of computational costs and benefits |
| topic | eQTL bayesian networks chemotherapy resistance Search algorithm Network variable selection Genetic data integration |
| url | http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00040/full |
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