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Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond

  • Galina GlazkoEmail author
  • Yasir Rahmatallah
  • Boris Zybailov
  • Frank Emmert-Streib
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1613)

Abstract

The analysis of gene sets (in a form of functionally related genes or pathways) has become the method of choice for extracting the strongest signals from omics data. The motivation behind using gene sets instead of individual genes is two-fold. First, this approach incorporates pre-existing biological knowledge into the analysis and facilitates the interpretation of experimental results. Second, it employs a statistical hypotheses testing framework. Here, we briefly review main Gene Set Analysis (GSA) approaches for testing differential expression of gene sets and several GSA approaches for testing statistical hypotheses beyond differential expression that allow extracting additional biological information from the data. We distinguish three major types of GSA approaches testing: (1) differential expression (DE), (2) differential variability (DV), and (3) differential co-expression (DC) of gene sets between two phenotypes. We also present comparative power analysis and Type I error rates for different approaches in each major type of GSA on simulated data. Our evaluation presents a concise guideline for selecting GSA approaches best performing under particular experimental settings. The value of the three major types of GSA approaches is illustrated with real data example. While being applied to the same data set, major types of GSA approaches result in complementary biological information.

Key words

Omics data Gene set analysis approaches Hypotheses testing Self-contained Competitive Differential expression Differential co-expression Differential variability 

Notes

Acknowledgments

We would like to thank Bárbara Macías Solís for proof reading of the manuscript. Support has been provided in part by the Arkansas INBRE program, with grants from the National Center for Research Resources (P20RR016460) and the National Institute of General Medical Sciences (P20 GM103429) from the National Institutes of Health. Large-scale computer simulations were implemented using the High Performance Computing (HPC) resources at the UALR Computational Research Center supported by the following grants: National Science Foundation grants CRI CNS-0855248, EPS-0701890, MRI CNS-0619069 and OISE-0729792.

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Galina Glazko
    • 1
    Email author
  • Yasir Rahmatallah
    • 1
  • Boris Zybailov
    • 2
  • Frank Emmert-Streib
    • 3
  1. 1.Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockUSA
  2. 2.Department of Biochemistry and Molecular BiologyUniversity of Arkansas for Medical SciencesLittle RockUSA
  3. 3.Computational Medicine and Statistical Learning LaboratoryTampere University of TechnologyTampereFinland

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