title: GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks.
abstract: CONCLUSIONS
  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 ('seed-genes') within a biological network of their choosing. Two methods are implemented for calculating the significance of connectivity among seed-genes: 'seed randomization' and 'network permutation'. 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 (∼10 million edges) on a desktop computer.
  
  
  METHODS
  GeneNet Toolbox is open source and freely available from http://avigailtaylor.github.io/gntat14.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
  
  
  BACKGROUND
  avigail.taylor@dpag.ox.ac.uk.
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Avigail
authors.initials: A
authors.lastname: Taylor
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Julia
authors.initials: J
authors.lastname: Steinberg
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Tallulah S
authors.initials: TS
authors.lastname: Andrews
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK and The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Caleb
authors.initials: C
authors.lastname: Webber
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D016247:Information Storage and Retrieval; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface