title: SorghumFDB: sorghum functional genomics database with multidimensional network analysis.
abstract: Sorghum (Sorghum bicolor [L.] Moench) has excellent agronomic traits and biological properties, such as heat and drought-tolerance. It is a C4 grass and potential bioenergy-producing plant, which makes it an important crop worldwide. With the sorghum genome sequence released, it is essential to establish a sorghum functional genomics data mining platform. We collected genomic data and some functional annotations to construct a sorghum functional genomics database (SorghumFDB). SorghumFDB integrated knowledge of sorghum gene family classifications (transcription regulators/factors, carbohydrate-active enzymes, protein kinases, ubiquitins, cytochrome P450, monolignol biosynthesis related enzymes, R-genes and organelle-genes), detailed gene annotations, miRNA and target gene information, orthologous pairs in the model plants Arabidopsis, rice and maize, gene loci conversions and a genome browser. We further constructed a dynamic network of multidimensional biological relationships, comprised of the co-expression data, protein-protein interactions and miRNA-target pairs. We took effective measures to combine the network, gene set enrichment and motif analyses to determine the key regulators that participate in related metabolic pathways, such as the lignin pathway, which is a major biological process in bioenergy-producing plants.Database URL: http://structuralbiology.cau.edu.cn/sorghum/index.html.
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors.forename: Tian
authors.initials: T
authors.lastname: Tian
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: You
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors.forename: Liwei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Yi
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors.forename: Hengyu
authors.initials: H
authors.lastname: Yan
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors.forename: Wenying
authors.initials: W
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China zhensu@cau.edu.cn.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Su
mesh_terms: D030541:Databases, Genetic; D017343:Genes, Plant / Q000502:physiology*; D023281:Genomics; D058977:Molecular Sequence Annotation; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D045868:Sorghum / Q000235:genetics / Q000378:metabolism; D064878:Web Browser
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant