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Related Concept Videos

Transcription Factors02:16

Transcription Factors

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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...
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Conserved Binding Sites01:49

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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...
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General Transcription Factors01:30

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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...
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Related Experiment Video

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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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RTFBSDB: an integrated framework for transcription factor binding site analysis.

Zhong Wang1, André L Martins1, Charles G Danko2

  • 1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.

Bioinformatics (Oxford, England)
|June 12, 2016
PubMed
Summary
This summary is machine-generated.

This study introduces rtfbsdb, a tool for analyzing transcription factor (TF) binding motifs. It efficiently scans genomes and integrates expression data to identify relevant TF binding sites for specific cell types.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transcription factors (TFs) are crucial regulators of gene transcription.
  • TF binding to DNA sequence motifs dictates gene expression patterns.
  • Analyzing TF binding sites across genomes is essential for understanding gene regulation.

Purpose of the Study:

  • To present rtfbsdb, a unified framework for TF binding motif analysis.
  • To provide tools for efficient scanning of target genome sequences for TF binding motifs.
  • To integrate TF expression data with motif analysis for cell-type-specific insights.

Main Methods:

  • Integration of a comprehensive database of over 65,000 TF binding motifs.
  • Development of tools for rapid and efficient scanning of genome sequences.
  • Clustering of motifs based on DNA sequence specificity.
  • Incorporation of RNA-seq or PRO-seq data to filter for expressed TFs.

Main Results:

  • rtfbsdb offers a unified framework for TF binding motif analysis.
  • The package facilitates efficient genome scanning for TF binding sites.
  • Motif clustering and integration of expression data enable cell-type-specific analyses.
  • Common TF binding analyses can be performed rapidly within an integrated environment.

Conclusions:

  • rtfbsdb provides an efficient and integrated solution for analyzing transcription factor binding motifs.
  • The framework supports cell-type-specific investigations by integrating TF expression data.
  • This tool streamlines complex genomic analyses related to gene regulation.