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Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated “Knowledge-Based” Platform

  • Alexey DubovenkoEmail author
  • Yuri Nikolsky
  • Eugene Rakhmatulin
  • Tatiana Nikolskaya
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1613)

Abstract

Analysis of NGS and other sequencing data, gene variants, gene expression, proteomics, and other high-throughput (OMICs) data is challenging because of its biological complexity and high level of technical and biological noise. One way to deal with both problems is to perform analysis with a high fidelity annotated knowledgebase of protein interactions, pathways, and functional ontologies. This knowledgebase has to be structured in a computer-readable format and must include software tools for managing experimental data, analysis, and reporting. Here, we present MetaCore™ and Key Pathway Advisor (KPA), an integrated platform for functional data analysis. On the content side, MetaCore and KPA encompass a comprehensive database of molecular interactions of different types, pathways, network models, and ten functional ontologies covering human, mouse, and rat genes. The analytical toolkit includes tools for gene/protein list enrichment analysis, statistical “interactome” tool for the identification of over- and under-connected proteins in the dataset, and a biological network analysis module made up of network generation algorithms and filters. The suite also features Advanced Search, an application for combinatorial search of the database content, as well as a Java-based tool called Pathway Map Creator for drawing and editing custom pathway maps. Applications of MetaCore and KPA include molecular mode of action of disease research, identification of potential biomarkers and drug targets, pathway hypothesis generation, analysis of biological effects for novel small molecule compounds and clinical applications (analysis of large cohorts of patients, and translational and personalized medicine).

Key words

Pathway analysis Functional analysis Systems biology Signaling and metabolic networks Biological networks “Knowledge-based” platform Interactome Causal reasoning 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Alexey Dubovenko
    • 1
    Email author
  • Yuri Nikolsky
    • 2
    • 3
  • Eugene Rakhmatulin
    • 1
  • Tatiana Nikolskaya
    • 4
  1. 1.Clarivate AnalyticsPhiladelphiaUSA
  2. 2.Prosapia GeneticsSolana BeachUSA
  3. 3.School of Systems BiologyGeorge Mason UniversityFairfaxUSA
  4. 4.RosGenDiagnostikaMoscowRussia

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