References
- Costa MOC, Nascimento APB, Martins YC, Santos MT, Figueiredo AMS, Perez-Rueda E, Nicolás MF. 2023. The gene regulatory network of Staphylococcus aureus ST239-SCCmecIII strain Bmb9393 and assessment of genes associated with the biofilm in diverse backgrounds. Frontiers in Microbiology. 13:1049819
- Flores-Bautista E, Hernandez-Guerrero R, Huerta-Saquero A, Tenorio-Salgado S, Rivera-Gomez N, Romero A, Ibarra JA, Perez-Rueda E. 2020. Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms. PLoS One. 15(8): e0237135
- Perez-Rueda E. Janga,S.C. 2010. Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin Mol Biol Evol. 27, 1449-1459
- Moreno-Campuzano,S. Chandra,J.S. Perez-Rueda E. 2006. Identification and analysis of DNA-binding Transcription Factors in Bacillus subtilis and other Firmicutes- A genomic approach BMC Genomics, 7, 147
- Perez-Rueda E, Collado-Vides J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli. Nucleic Acids Research. 28, 1838-1847
About EnTRaF
The DNA-binding transcription factors (TFs) have a fundamental role to contend with environmental changes in all the organisms. These proteins affect gene expression positively and/or negatively depending on operator context and ligand-binding status. Prediction and characterization of novel TFs generally involve finding a function for a protein considering a reference dataset (golden standard), which include the information of well-annotated proteins with experimental evidence.
ENTRAF provides a centralized, web-based location to organize information about 1784 TFs with experimental evidence, from bacteria and archaea organisms, collected from Swissprot, PDB, RegulonDB, RegulomeDB, CollecTF, and DBTBS.
ENTRAF version 2.0 contains 2787 references associated with 1784 Transcription factors (TFs). From these, 1712 TFs have been characterized in 29 bacterial orders, such as Gammaproteobacteria, Bacilli, and Actinomycetota; and 72 TFs in ten archaeal orders, as Thermoprotei and Thermococci.