title: From manual curation to visualization of gene families and networks across Solanaceae plant species.
abstract: High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants. Database URL: http://solgenomics.net/
authors.affiliation: Boyce Thompson Institute for Plant Research, 533, Tower Road, Ithaca, NY 14853, USA.
authors.forename: Anuradha
authors.initials: A
authors.lastname: Pujar
authors.forename: Naama
authors.initials: N
authors.lastname: Menda
authors.forename: Aureliano
authors.initials: A
authors.lastname: Bombarely
authors.forename: Jeremy D
authors.initials: JD
authors.lastname: Edwards
authors.forename: Susan R
authors.initials: SR
authors.lastname: Strickler
authors.forename: Lukas A
authors.initials: LA
authors.lastname: Mueller
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D057225:Data Mining / Q000379:methods*; D055864:Droughts; D053263:Gene Regulatory Networks / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics*; D005819:Genetic Markers; D058977:Molecular Sequence Annotation; D005810:Multigene Family / Q000235:genetics*; D019657:Solanaceae / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D005819:Genetic Markers