swMATH ID: 17023
Software Authors: Jin, J.; Tian, F.; Yang, D. C.; Meng, Y. Q.; Kong, L.; Luo, J.; Gao, G.
Description: PlantTFDB. Plant Transcription Factor Database. Based on the family assignment rules, we identified 320,370 transcription factors from 165 species and classified them into 58 families. Species included in PlantTFDB 4.0 covers the main lineages of green plants, providing genomic TF repertoires across green plants. To provide comprehensive information for the TF family, a brief introduction and key references are presented for each family. Comprehensive annotations are made for each identified TF, including functional domains, 3D structures, gene ontology (GO), plant ontology (PO), expression information, expert-curated functional description, binding motifs, regulation information, interaction, references, and cross-linsk to various databases such as UniProt, RefSeq, STRING and Entrez Gene. By inferring orthologous groups and constructing phylogenetic trees, evolutionary relationships among identified TFs were inferred. In addition, PlantTFDB has a simple and user-friendly interface to allow users to query using TF IDs and common names in Quick Search, or sequences in BLAST. A TF prediction server, which supports both protein and nucleic acid sequences, has been set up for users to identify TFs from multiple sequences (file up to 100M). Users can access the regulation data and tools for regulation prediction and functional enrichment analyses at our new portal PlantRegMap, and access the the architecture and evolutionary features of plant transcriptional regulatory networks at ATRM (Brief Guide in English and Chinese).
Homepage: http://planttfdb.cbi.pku.edu.cn/
Related Software: R; sva; Matrix eQTL; JASPAR; UniProt; FIMO; KEGG; KLU; FATODE; RegulonDB; GeneNetWeaver; SIRENE; NOMAD; Path2Models; SOSlib; LASSIE; BioPreDyn-bench; MMG; sgnesR; GeNGe
Cited in: 2 Documents

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