{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T12:30:27Z","timestamp":1766579427575},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"vor","delay-in-days":751,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary : We present GeneNet Toolbox for MATLAB (also available as a set of standalone applications for Linux). The toolbox, available as command-line or with a graphical user interface, enables biologists to assess connectivity among a set of genes of interest (\u2018seed-genes\u2019) within a biological network of their choosing. Two methods are implemented for calculating the significance of connectivity among seed-genes: \u2018seed randomization\u2019 and \u2018network permutation\u2019. Options include restricting analyses to a specified subnetwork of the primary biological network, and calculating connectivity from the seed-genes to a second set of interesting genes. Pre-analysis tools help the user choose the best connectivity-analysis algorithm for their network. The toolbox also enables visualization of the connections among seed-genes. GeneNet Toolbox functions execute in reasonable time for very large networks (\u223c10 million edges) on a desktop computer.<\/jats:p>\n               <jats:p>Availability and implementation : GeneNet Toolbox is open source and freely available from http:\/\/avigailtaylor.github.io\/gntat14 .<\/jats:p>\n               <jats:p>Supplementary information : Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Contact: \u00a0avigail.taylor@dpag.ox.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu669","type":"journal-article","created":{"date-parts":[[2014,10,16]],"date-time":"2014-10-16T01:58:54Z","timestamp":1413424734000},"page":"442-444","source":"Crossref","is-referenced-by-count":13,"title":["GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks"],"prefix":"10.1093","volume":"31","author":[{"given":"Avigail","family":"Taylor","sequence":"first","affiliation":[{"name":"1 MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and 2 The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julia","family":"Steinberg","sequence":"additional","affiliation":[{"name":"1 MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and 2 The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK"},{"name":"1 MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and 2 The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tallulah S.","family":"Andrews","sequence":"additional","affiliation":[{"name":"1 MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and 2 The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caleb","family":"Webber","sequence":"additional","affiliation":[{"name":"1 MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and 2 The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,10,14]]},"reference":[{"key":"2023020116160410200_btu669-B1","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/1471-2105-13-226","article-title":"Network enrichment analysis: extension of gene-set enrichment analysis to gene networks","volume":"13","author":"Alexeyenko","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023020116160410200_btu669-B2","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1007\/BF02289146","article-title":"A method of matrix analysis of group structure","volume":"14","author":"Luce","year":"1949","journal-title":"Psychometrika"},{"key":"2023020116160410200_btu669-B3","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1126\/science.1065103","article-title":"Specificity and stability in topology of protein networks","volume":"296","author":"Maslov","year":"2002","journal-title":"Science"},{"key":"2023020116160410200_btu669-B4","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1745-6150-4-14","article-title":"Transcript length bias in RNA-seq data confounds systems biology","volume":"4","author":"Oshlack","year":"2009","journal-title":"Biol. 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