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Knowledge-Based Compact Disease Models: A Rapid Path from High-Throughput Data to Understanding Causative Mechanisms for a Complex Disease

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Biological Networks and Pathway Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1613))

Abstract

High-throughput profiling of human tissues typically yields the gene lists composed of a variety of more or less relevant molecular entities. These lists are riddle by false positive observations that often obstruct generation of mechanistic hypothesis that may explain complex phenotype. From general probabilistic considerations, the gene lists enriched by the mechanistically relevant targets can be far more useful for subsequent experimental design or data interpretation. Using Alzheimer’s disease as example, the candidate gene lists were processed into different tiers of evidence consistency established by enrichment analysis across subdatasets collected within the same experiment and across different experiments and platforms. The cutoffs were established empirically through ontological and semantic enrichment; resultant shortened gene list was reexpanded by Ingenuity Pathway Assistant tool. The resulting subnetworks provided the basis for generating mechanistic hypotheses that were partially validated by mined experimental evidence. This approach differs from previous consistency-based studies in that the cutoff on the Receiver Operating Characteristic of the true–false separation process is optimized by flexible selection of the consistency building procedure. The resultant Compact Disease Models (CDM) composed of the gene list distilled by this analytic technique and its network-based representation allowed us to highlight possible role of the protein traffic vesicles in the pathogenesis of Alzheimer’s. Considering the distances and complexity of protein trafficking in neurons, it is plausible to hypothesize that spontaneous protein misfolding along with a shortage of growth stimulation may provide a shortcut to neurodegeneration. Several potentially overlapping scenarios of early-stage Alzheimer pathogenesis are discussed, with an emphasis on the protective effects of Angiotensin receptor 1 (AT-1) mediated antihypertensive response on cytoskeleton remodeling, along with neuronal activation of oncogenes, luteinizing hormone signaling and insulin-related growth regulation, forming a pleiotropic model of its early stages. Compact Disease Model generation is a flexible approach for high-throughput data analysis that allows extraction of meaningful, mechanism-centered gene sets compatible with instant translation of the results into testable hypotheses.

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Acknowledgments

The authors express their gratitude to the general support provided by College of Science, George Mason University and the Human Proteome Project Program of the Russian Academy of Medical Sciences.

Authors’ Contributions

Both authors contributed to the study design, interpretation of results, and producing the manuscript. All the authors read and approved the final manuscript.

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Authors and Affiliations

  1. The Center of the Study of Chronic Metabolic and Rare Diseases, School of Systems Biology, College of Science, George Mason University, Fairfax, VA, 22030, USA

    Anatoly Mayburd & Ancha Baranova

  2. Research Centre for Medical Genetics, RAMS, Moskvorechie 1, Moscow, Russia

    Ancha Baranova

Authors
  1. Anatoly Mayburd
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  2. Ancha Baranova
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Corresponding author

Correspondence to Ancha Baranova .

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Editors and Affiliations

  1. Keck School of Medicine, University of Southern California, Los Angeles, California, USA

    Tatiana V. Tatarinova

  2. Prosapia Genetics, Solana Beach, California, USA

    Yuri Nikolsky

1 Electronic Supplementary Materials

Additional file 1

Datasets A, B, and C: (the primary data). Dataset D: Tiered consistency scores for all scored genes (XLS 324 kb)

Additional file 2

The outputs of GO -MINER ontological analysis of the genes within Consistency Tier 0 (XLS 3257 kb)

Additional file 3

The outputs of GO-MINER ontological analysis of the genes within Consistency Tier 1 (XLS 1622 kb)

Additional file 4

The outputs of GO-MINER ontological analysis of the genes within Consistency Tier 2 (XLS 1630 kb)

Additional file 5

The outputs of GO-MINER ontological analysis of the genes within Consistency Tier 3 (XLS 1634 kb)

Additional file 6

The subnetwork composition for the Tier 1, including both experimental and inferred members (XLS 31 kb)

Additional file 7

The subnetwork composition for the Tiers 1–3, including both experimental and inferred members (XLS 38 kb)

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Mayburd, A., Baranova, A. (2017). Knowledge-Based Compact Disease Models: A Rapid Path from High-Throughput Data to Understanding Causative Mechanisms for a Complex Disease. In: Tatarinova, T., Nikolsky, Y. (eds) Biological Networks and Pathway Analysis. Methods in Molecular Biology, vol 1613. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7027-8_17

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  • DOI: https://doi.org/10.1007/978-1-4939-7027-8_17

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  • Online ISBN: 978-1-4939-7027-8

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