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Integrated Analysis of Transcriptomic and Proteomic Datasets Reveals Information on Protein Expressivity and Factors Affecting Translational Efficiency

  • Jiangxin Wang
  • Gang Wu
  • Lei Chen
  • Weiwen ZhangEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1375)

Abstract

Integrated analysis of large-scale transcriptomic and proteomic data can provide important insights into the metabolic mechanisms underlying complex biological systems. In this chapter, we present methods to address two aspects of issues related to integrated transcriptomic and proteomic analysis. First, due to the fact that proteomic datasets are often incomplete, and integrated analysis of partial proteomic data may introduce significant bias. To address these issues, we describe a zero-inflated Poisson (ZIP)-based model to uncover the complicated relationships between protein abundances and mRNA expression levels, and then apply them to predict protein abundance for the proteins not experimentally detected. The ZIP model takes into consideration the undetected proteins by assuming that there is a probability mass at zero representing expressed proteins that were undetected owing to technical limitations. The model validity is demonstrated using biological information of operons, regulons, and pathways. Second, weak correlation between transcriptomic and proteomic datasets is often due to biological factors affecting translational processes. To quantify the effects of these factors, we describe a multiple regression-based statistical framework to quantitatively examine the effects of various translational efficiency-related sequence features on mRNA–protein correlation. Using the datasets from sulfate-reducing bacteria Desulfovibrio vulgaris, the analysis shows that translation-related sequence features can contribute up to 15.2–26.2 % of the total variation of the correlation between transcriptomic and proteomic datasets, and also reveals the relative importance of various features in translation process.

Keywords

Transcriptome Proteome Correlation Zero-inflated Poisson regression Prediction Undetected proteins Translation Sequence features 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Jiangxin Wang
    • 1
    • 2
    • 3
  • Gang Wu
    • 4
  • Lei Chen
    • 1
    • 2
    • 3
  • Weiwen Zhang
    • 1
    • 2
    • 3
    Email author
  1. 1.Laboratory of Synthetic Microbiology, School of Chemical Engineering and TechnologyTianjin UniversityTianjinPeople’s Republic of China
  2. 2.Key Laboratory of Systems BioengineeringMinistry of Education of ChinaTianjinPeople’s Republic of China
  3. 3.Collaborative Innovation Center of Chemical Science and EngineeringTianjinPeople’s Republic of China
  4. 4.University of Maryland at Baltimore CountryBaltimore CountyUSA

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