FlyNet: a versatile network prioritization server for theDrosophilacommunity

Abstract

Drosophila melanogaster (fruit fly) has been a popular model organism in animal genetics due to the high accessibility of reverse-genetics tools. In addition, the close relationship between the Drosophila and human genomes rationalizes the use of Drosophila as an invertebrate model for human neurobiology and disease research. A platform technology for predicting candidate genes or functions would further enhance the usefulness of this long-established model organism for gene-to-phenotype mapping. Recently, the power of network prioritization for gene-to-phenotype mapping has been demonstrated in many organisms. Here we present a network prioritization server dedicated to Drosophila that covers ∼95% of the coding genome. This server, dubbed FlyNet, has several distinctive features, including (i) prioritization for both genes and functions; (ii) two complementary network algorithms: direct neighborhood and network diffusion; (iii) spatiotemporal-specific networks as an additional prioritization strategy for traits associated with a specific developmental stage or tissue and (iv) prioritization for human disease genes. FlyNet is expected to serve as a versatile hypothesis-generation platform for genes and functions in the study of basic animal genetics, developmental biology and human disease. FlyNet is available for free at http://www.inetbio.org/flynet.

Predictability of Genetic Interactions from Functional Gene Modules

“…All genetic interactions were downloaded from version 3.4.130 of BIOGRID [Stark et al, 2006]. Organism-specific functional gene networks were downloaded for human [Lee et al, 2011], fly [Shin et al, 2015], and yeast [Lee et al, 2007]. Previous studies served as sources of protein complexes for yeast and human [Hart et al, 2007, Ruepp et al, 2010].…”

SoyNet: a database of co-functional networks for soybeanGlycine max

“…(ii) Networks inferred by genomic context similarity based on either gene neighborhood across bacterial genomes (14) or similarity of phylogenetic profiles (15), using 396 eukaryotic genomes and 1748 prokaryotic genomes. (iii) Networks inferred from evolutionarily conserved functional associations (associalogs) (16) in seven other species: Arabidopsis thaliana (17), Caenorhabditis elegans (18), Drosophila melanogaster (19), Danio rerio, Homo sapiens (20), Saccharomyces cerevisiae (21) and Oryza sativa (22). We transferred co-expression links, protein-protein interactions derived from the literature and high-throughput analysis, and genetic interactions, based on orthology relationships as measured by Inpranoid software version 4.1 (23).…”

WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum

“…Similarly, associalogs are conserved functional associations between genes whose orthologs in other organisms are also functionally coupled. WheatNet component networks based on associalogs were transferred from our previously published networks for seven organisms: YeastNet for Saccharomyces cerevisiae , AraNet for Arabidopsis 6 thaliana (Lee et al, 2015c), RiceNet for Oryza sativa (Lee et al, 2015b), FlyNet for Drosophila melanogaster (Shin et al, 2015), WormNet for Caenorhabditis elegans (Cho et al, 2014), DanioNet for Danio rerio , MouseNet for Mus musculus , and HumanNet for Homo sapiens (Lee et al, 2011). In addition, associalogs from an unpublished functional network for Zea mays were integrated into WheatNet.…”

“…drafted the manuscript. P.C.R., and E.M.M., edited the manuscript 9. Upadhyay, S.K., Kumar, J., Alok, A., and Tuli, R. (2013).…”