{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T23:41:49Z","timestamp":1722728509122},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Systems Genetics approaches, in particular those relying on genetical genomics data, put forward a new paradigm of large-scale genome and network analysis. These methods use naturally occurring multi-factorial perturbations (e.g. polymorphisms) in properly controlled and screened genetic crosses to elucidate causal relationships in biological networks. However, although genetical genomics data contain rich information, a clear dissection of causes and effects as required for reconstructing gene regulatory networks is not easily possible.<\/jats:p><jats:p>Results: We present a framework for reconstructing gene regulatory networks from genetical genomics data where genotype and phenotype correlation measures are used to derive an initial graph which is subsequently reduced by pruning strategies to minimize false positive predictions. Applied to realistic simulated genetic data from a recent DREAM challenge, we demonstrate that our approach is simple yet effective and outperforms more complex methods (including the best performer) with respect to (i) reconstruction quality (especially for small sample sizes) and (ii) applicability to large data sets due to relatively low computational costs. We also present reconstruction results from real genetical genomics data of yeast.<\/jats:p><jats:p>Availability: A MATLAB implementation (script) of the reconstruction framework is available at www.mpi-magdeburg.mpg.de\/projects\/cna\/etcdownloads.html<\/jats:p><jats:p>Contact: \u00a0klamt@mpi-magdeburg.mpg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts679","type":"journal-article","created":{"date-parts":[[2012,11,23]],"date-time":"2012-11-23T03:52:09Z","timestamp":1353642729000},"page":"246-254","source":"Crossref","is-referenced-by-count":10,"title":["An effective framework for reconstructing gene regulatory networks from genetical genomics data"],"prefix":"10.1093","volume":"29","author":[{"given":"R. J.","family":"Flassig","sequence":"first","affiliation":[{"name":"1 Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1 and 2Otto-von-Guericke University, Universit\u00e4tsplatz 2, 39106 Magdeburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S.","family":"Heise","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1 and 2Otto-von-Guericke University, Universit\u00e4tsplatz 2, 39106 Magdeburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"K.","family":"Sundmacher","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1 and 2Otto-von-Guericke University, Universit\u00e4tsplatz 2, 39106 Magdeburg, Germany"},{"name":"1 Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1 and 2Otto-von-Guericke University, Universit\u00e4tsplatz 2, 39106 Magdeburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S.","family":"Klamt","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1 and 2Otto-von-Guericke University, Universit\u00e4tsplatz 2, 39106 Magdeburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,11,21]]},"reference":[{"key":"2023012810165210800_bts679-B1","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1534\/genetics.105.041103","article-title":"Genetical genomic analysis of a yeast segregant population for transcription network inference","volume":"170","author":"Bing","year":"2005","journal-title":"Genetics"},{"key":"2023012810165210800_bts679-B2","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1016\/S0167-7799(02)02053-X","article-title":"Gene networks: how to put the function in genomics","volume":"20","author":"Brazhnik","year":"2002","journal-title":"Trends Biotechnol"},{"key":"2023012810165210800_bts679-B3","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random forests","volume":"45","author":"Breitman","year":"2001","journal-title":"Machine Learning"},{"key":"2023012810165210800_bts679-B4","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1073\/pnas.0408709102","article-title":"The landscape of genetic complexity across 5,700 gene expression traits in yeast","volume":"102","author":"Brem","year":"2005","journal-title":"PNAS"},{"key":"2023012810165210800_bts679-B5","doi-asserted-by":"crossref","first-page":"2383","DOI":"10.1093\/bioinformatics\/bti241","article-title":"Methodological aspects of the genetic dissection of gene expression","volume":"21","author":"Carlborg","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012810165210800_bts679-B6","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1093\/genetics\/138.3.963","article-title":"Empirical threshold values for quantitative trait mapping","volume":"138","author":"Churchill","year":"1994","journal-title":"Genetics"},{"key":"2023012810165210800_bts679-B7","article-title":"Learning the structure of dynamic probabilistic networks","author":"Friedmann","year":"1998"},{"key":"2023012810165210800_bts679-B8","doi-asserted-by":"crossref","DOI":"10.4018\/978-1-60566-685-3.ch001","article-title":"What are Gene Regulatory Networks?","volume-title":"Computational Methodologies in Gene Regulatory Networks","author":"de la Fuente","year":"2010"},{"key":"2023012810165210800_bts679-B9","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/S0168-9525(01)02310-1","article-title":"Genetical genomics: the added value from segregation","volume":"17","author":"Jansen","year":"2001","journal-title":"Trends Genet."},{"key":"2023012810165210800_bts679-B10","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/nrg996","article-title":"Studying complex biological systems using multifactorial perturbation","volume":"4","author":"Jansen","year":"2003","journal-title":"Nat. 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