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Updated: Aug 7, 2026
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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
Published on: February 7, 2019
POXO: a web-enabled tool series to discover transcription factor binding sites
Matti Kankainen1, Petri Pehkonen, Päivi Rosenstöm
1Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 5), FIN-00014 Helsinki, Finland.
Nucleic Acids Research
|July 18, 2006
Summary
POXO is a new tool series for identifying transcription factor binding sites in co-expressed genes. It helps researchers analyze gene functions and discover regulatory patterns, aiding in understanding gene regulation.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Identifying transcription factor binding sites is crucial for understanding gene regulation.
- Co-expressed genes often share common regulatory elements.
- Existing tools may lack comprehensive pipelines for integrated analysis.
Purpose of the Study:
- To introduce POXO, a versatile tool series for discovering transcription factor binding sites from co-expressed genes.
- To provide a user-friendly platform for tailoring analytical pipelines for gene expression data.
- To facilitate the identification of cis-regulatory elements and co-regulated genes.
Main Methods:
- Functional evaluation and grouping of co-expressed genes.
- Sequence retrieval and over-represented nucleotide pattern discovery.
- Pattern verification and clustering of similar motifs.
- Pipeline customization through a graphical interface.
Main Results:
- POXO successfully identified activated gene sets in pathogen-treated Arabidopsis thaliana.
- The tool suggested potential transcription factors responsible for regulating these gene sets.
- Demonstrated the utility of POXO in analyzing gene expression data and inferring regulatory mechanisms.
Conclusions:
- POXO offers a comprehensive and integrated approach to discover transcription factor binding sites.
- The tool aids in understanding gene co-regulation and identifying key regulatory elements.
- POXO provides a valuable resource for researchers in genomics and systems biology.
Related Concept Videos
02:16Transcription Factors
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
02:16Transcription Factors
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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...
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...
01:30General Transcription Factors
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
02:13Cooperative Binding of Transcription Regulators
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
02:13Cooperative Binding of Transcription Regulators
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...