Related Experiment Video
Updated: Jul 17, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
Published on: February 7, 2019
Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs
1Department of Biostatistics, Bioinformatics and Epidemiology, and Bioinformatics Core Facility, Hollings Cancer Center, Medical University of South Carolina, 135 Cannon Street, Charleston, SC 29425, USA. maol@musc.edu
Background:
As more and more genomes are sequenced, comparative genomics approaches provide a methodology for identifying conserved regulatory elements that may be involved in gene regulations.
Results:
We developed a novel method to combine comparative genomics with de novo motif discovery to identify human transcription factor binding motifs that are overrepresented and conserved in the upstream regions of a set of co-regulated genes. The method is validated by analyzing a well-characterized muscle specific gene set, and the results showed that our approach performed better than the existing programs in terms of sensitivity and prediction rate.
Conclusion:
The newly developed method can be used to extract regulatory signals in co-regulated genes, which can be derived from the microarray clustering analysis.
Related Concept Videos
Cooperative Binding of Transcription Regulators
Cooperative Binding of Transcription Regulators
Combinatorial Gene Control
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
Transcription Factors
Transcription Factors
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

