ArticleBMC plant biology2010
SoyDB: a knowledge database of soybean transcription factors.
Article in BMC plant biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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56 citing papers in PubMed, 126 citations in OpenAlex.
- Decoding the landscape of cell-type-specific co-expressed transcription factors in soybean.Nature plants · 2026Article
- GmGLU1 and GmRR4 contribute to iron deficiency tolerance in soybean.Frontiers in plant science · 2024Article
- Coupling VIGS with Short- and Long-Term Stress Exposure to Understand the Fiskeby III Iron Deficiency Stress Response.International journal of molecular sciences · 2022Article
- Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids.BMC genomics · 2021Article
- Comparing Early Transcriptomic Responses of 18 Soybean (International journal of molecular sciences · 2021Article
- Mining Fiskeby III and Mandarin (Ottawa) Expression Profiles to Understand Iron Stress Tolerant Responses in Soybean.International journal of molecular sciences · 2021Article
- Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean.International journal of molecular sciences · 2021Article
- CamRegBase: a gene regulation database for the biofuel crop, Camelina sativa.Database : the journal of biological databases and curation · 2020Article
- New tools for characterizing early brown stem rot disease resistance signaling in soybean.The plant genome · 2020Article
- Examining Short-Term Responses to a Long-Term Problem: RNA-Seq Analyses of Iron Deficiency Chlorosis Tolerant Soybean.International journal of molecular sciences · 2020Article
- Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean.Functional & integrative genomics · 2020Article
- The MAPK Kinase Kinase GmMEKK1 Regulates Cell Death and Defense Responses.Plant physiology · 2018Article
- SoyNet: a database of co-functional networks for soybean Glycine max.Nucleic acids research · 2017Article
- Transcription factors involved in drought tolerance and their possible role in developing drought tolerant cultivars with emphasis on wheat (Triticum aestivum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Review
- Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae).Scientific reports · 2016Article
- Genome-wide identification of soybean WRKY transcription factors in response to salt stress.SpringerPlus · 2016Article
- Soybean transcription factor ORFeome associated with drought resistance: a valuable resource to accelerate research on abiotic stress resistance.BMC genomics · 2015Article
- Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response.Molecular genetics and genomics : MGG · 2015Article
- Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining.Rice (New York, N.Y.) · 2015Article
- A classification of basic helix-loop-helix transcription factors of soybean.International journal of genomics · 2015Article
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Authors and funding
8 authors at 1 institution in 1 country.
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Abstract
backgroundTranscription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors. DESCRIPTION: The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI) and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database for all the transcription factors in the soybean genome. The database contains protein sequences, predicted tertiary structures, putative DNA binding sites, domains, homologous templates in the Protein Data Bank (PDB), protein family classifications, multiple sequence alignments, consensus protein sequence motifs, web logo of each family, and web links to the soybean transcription factor database PlantTFDB, known EST sequences, and other general protein databases including Swiss-Prot, Gene Ontology, KEGG, EMBL, TAIR, InterPro, SMART, PROSITE, NCBI, and Pfam. The database can be accessed via an interactive and convenient web server, which supports full-text search, PSI-BLAST sequence search, database browsing by protein family, and automatic classification of a new protein sequence into one of 64 annotated transcription factor families by hidden Markov models.
conclusionsA comprehensive soybean transcription factor database was constructed and made publicly accessible at http://casp.rnet.missouri.edu/soydb/.
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