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Related Concept Videos

Transcription Factors02:16

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...

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Related Experiment Video

Updated: Jul 13, 2026

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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LBFextract: Unveiling transcription factor dynamics from liquid biopsy data.

Isaac Lazzeri1, Benjamin Gernot Spiegl1, Samantha O Hasenleithner2

  • 1Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstr. 6, Graz 8010, Austria.

Computational and Structural Biotechnology Journal
|December 11, 2024
PubMed
Summary

Liquid Biopsy Feature extract (LBFextract) is a new bioinformatics package for analyzing cell-free DNA (cfDNA) data. It improves reproducibility in liquid biopsy studies by streamlining feature extraction for biomarker discovery and disease classification.

Keywords:
BioinformaticsCell-free DNAFragmentomicsTranscription factorsWhole-genome sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Circulating cell-free DNA (cfDNA) analysis offers a non-invasive diagnostic approach for various conditions.
  • Extracting biological insights from cfDNA requires complex bioinformatics, considering DNA sequence, fragment length, nucleosome footprints, and methylation patterns.

Purpose of the Study:

  • To introduce Liquid Biopsy Feature extract (LBFextract), a package designed to standardize and simplify feature extraction from cfDNA sequencing data.
  • To enhance the reproducibility and comparability of liquid biopsy studies through integrated preprocessing and postprocessing.

Main Methods:

  • LBFextract integrates preprocessing and postprocessing using alignment fragment tags and a hook mechanism.
  • It employs coverage-based, fragment length-based, and novel entropy-based methods for TF activity inference and nucleosome dyad signal amplification.
  • Includes methods for extracting condition-specific differentially active TFs for biomarker discovery.

Main Results:

  • Demonstrated LBFextract's utility in classifying advanced prostate cancer subtypes using cfDNA coverage signals at TF binding sites.
  • Showcased LBFextract's ability to generate robust, interpretable features for discriminating between clinical groups.
  • Confirmed LBFextract as a versatile tool for liquid biopsy data analysis and interpretation.

Conclusions:

  • LBFextract provides a user-friendly solution for complex cfDNA data analysis.
  • The package facilitates biomarker discovery and enhances the clinical utility of liquid biopsies.
  • LBFextract promotes standardization and reproducibility in the field of liquid biopsy research.