GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks | Zendy

Avigail Taylor | Zendy; Julia Steinberg | Zendy; Tallulah Andrews | Zendy; Caleb Webber | Zendy

AI Assistant Blog Pricing

Home ZAIA Blog

Open Access

GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks

Author(s) -

Avigail Taylor,

Julia Steinberg,

Tallulah Andrews,

Caleb Webber

Publication year - 2014

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btu669

Subject(s) - toolbox , subnetwork , computer science , graphical user interface , matlab , set (abstract data type) , permutation (music) , visualization , data mining , gene regulatory network , biological network , software , interface (matter) , bioinformatics , gene , programming language , computer network , operating system , biology , biochemistry , gene expression , physics , acoustics , bubble , maximum bubble pressure method

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.

The content you want is available to Zendy users.

Already have an account? Click here to sign in.

Having issues? You can contact us here

Accelerating Research