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Related Experiment Videos

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.

Mohammed El-Kebir1, Hayssam Soueidan2, Thomas Hume3

  • 1Life Sciences, Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU, VU University Amsterdam, The Netherlands, Center for Computational Molecular Biology, Brown University, Providence, RI, USA.

Bioinformatics (Oxford, England)
|May 30, 2015
PubMed
Summary

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We developed a new model to find conserved gene networks between species, crucial for understanding diseases like those involving T helper 17 (Th17) cells. Our findings show key Th17 cell differentiation mechanisms are conserved between humans and mice.

Area of Science:

  • Computational Biology
  • Systems Biology
  • Immunology

Background:

  • Integrative network analysis is vital for interpreting high-throughput molecular data in biomedical research.
  • Translating findings from animal or cellular models to human applications remains a challenge.
  • Interleukin-17 producing helper T cells (Th17) are critical for immunity and implicated in autoimmune diseases.

Purpose of the Study:

  • To develop a mathematical model for identifying conserved active subnetwork modules between two species.
  • To create an algorithm for finding provably optimal or near-optimal conserved active modules.
  • To apply this model to understand conserved mechanisms in Th17 T cell differentiation.

Main Methods:

  • Proposed a mathematical model defining conserved modules based on network connectivity, differential behavior, and orthologous genes.

Related Experiment Videos

  • Introduced a flexible definition of conservation to enhance biological interpretability.
  • Developed an algorithm guaranteeing optimal or near-optimal solutions for conserved active modules.

    • Main Results:

    • Successfully identified conserved active subnetwork modules between species.
    • Applied the algorithm to analyze Th17 T cell differentiation in mouse and human models.
    • Discovered that key regulatory mechanisms of Th17 differentiation are conserved across species.

    Conclusions:

    • The developed model and algorithm effectively identify conserved biological modules.
    • The study provides significant insights into the conserved regulation of Th17 cell differentiation.
    • This approach facilitates cross-species comparative analysis for hypothesis generation and biomarker discovery.