Similarity regression predicts evolution of transcription factor sequence specificity

• Published in: Nature genetics Vol. 51; no. 6; pp. 981 - 989
• Main Authors: Lambert, Samuel A., Yang, Ally W. H., Sasse, Alexander, Cowley, Gwendolyn, Albu, Mihai, Caddick, Mark X., Morris, Quaid D., Weirauch, Matthew T., Hughes, Timothy R.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.06.2019; Nature Publishing Group
• Subjects: 45; 631/114; 631/1647/48; 631/208/191; 631/208/200; 64; 82; 82/80; Agriculture; Amino acids; Analysis; Animal Genetics and Genomics; Binding; Binding sites; Biomedical and Life Sciences; Biomedicine; Cancer Research; Deoxyribonucleic acid; Divergence; Diversification; DNA; DNA methylation; DNA-ligand interactions; Eukaryotes; Evolution; Fruit flies; Gene expression; Gene Function; Gene regulation; Generalized linear models; Genetic regulation; Genomes; Human Genetics; Insects; Predictions; Proteins; Regression analysis; Similarity; Transcription factors; Zinc finger proteins

Transcription factor (TF) binding specificities (motifs) are essential for the analysis of gene regulation. Accurate prediction of TF motifs is critical, because it is infeasible to assay all TFs in all sequenced eukaryotic genomes. There is ongoing controversy regarding the degree of motif diversif...