PECAplus: statistical analysis of time-dependent regulatory changes in dynamic single-omics and dual-omics experiments

Guoshou Teo, Yun Bin Zhang, Christine Vogel, Hyungwon Choi

Research output: Contribution to journalArticle

Abstract

Simultaneous dynamic profiling of mRNA and protein expression is increasingly popular, and there is a critical need for algorithms to identify regulatory layers and time dependency of gene expression. A group of scientists from United States and Singapore present PECAplus, a comprehensive set of statistical analysis tools to address this challenge. Protein expression control analysis (PECA) computes the probability scores for change in mRNA and protein-level regulatory parameters at each time point, deconvoluting gene expression regulation in the presence of measurement noise. PECAplus adapted PECA’s mass action model to a variety of proteomic data including pulsed SILAC and generic protein expression data. It also features analysis modules to fit smooth curves on rugged time series observations, and to facilitate time-dependent interpretation of the data for genes and biological functions. They demonstrate the core modules with two time course datasets of mammalian cells responding to unfolded proteins and pathogens.

Original languageEnglish (US)
Article number3
Journalnpj Systems Biology and Applications
Volume4
Issue number1
DOIs
StatePublished - Dec 1 2018

Fingerprint

Statistical Analysis
Statistical methods
Proteins
Protein
Experiment
Messenger RNA
Experiments
Gene Expression
Gene expression regulation
Module
Protein Unfolding
Singapore
Proteomics
Gene Expression Regulation
Pathogens
Profiling
Gene expression
Noise
Time series
Genes

ASJC Scopus subject areas

  • Computer Science Applications
  • Applied Mathematics
  • Modeling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Drug Discovery

Cite this

PECAplus : statistical analysis of time-dependent regulatory changes in dynamic single-omics and dual-omics experiments. / Teo, Guoshou; Bin Zhang, Yun; Vogel, Christine; Choi, Hyungwon.

In: npj Systems Biology and Applications, Vol. 4, No. 1, 3, 01.12.2018.

Research output: Contribution to journalArticle

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