Laguerre filter analysis with partial least square regression reveals a priming effect of ERK and CREB on c-FOS induction

Takamasa Kudo, Shinsuke Uda, Takaho Tsuchiya, Takumi Wada, Yasuaki Karasawa, Masashi Fujii, Takeshi H. Saito, Shinya Kuroda

Research output: Contribution to journalArticle

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Abstract

Signaling networks are made up of limited numbers of molecules and yet can code information that controls different cellular states through temporal patterns and a combination of signaling molecules. In this study, we used a data-driven modeling approach, the Laguerre filter with partial least square regression, to describe how temporal and combinatorial patterns of signaling molecules are decoded by their downstream targets. The Laguerre filter is a time series model used to represent a nonlinear system based on Volterra series expansion. Furthermore, with this approach, each component of the Volterra series expansion is expanded by Laguerre basis functions. We combined two approaches, application of a Laguerre filter and partial least squares (PLS) regression, and applied the combined approach to analysis of a signal transduction network.We applied the Laguerre filter with PLS regression to identify input and output (IO) relationships between MAP kinases and the products of immediate early genes (IEGs).We found that Laguerre filter with PLS regression performs better than Laguerre filter with ordinary regression for the reproduction of a time series of IEGs. Analysis of the nonlinear characteristics extracted using the Laguerre filter revealed a priming effect of ERK and CREB on c-FOS induction. Specifically, we found that the effects of a first pulse of ERK enhance the subsequent effects on c-FOS induction of treatment with a second pulse of ERK, a finding consistent with prior molecular biological knowledge. The variable importance of projections and output loadings in PLS regression predicted the upstream dependency of each IEG. Thus, a Laguerre filter with partial least square regression approach appears to be a powerful method to find the processing mechanism of temporal patterns and combination of signaling molecules by their downstream gene expression.

Original languageEnglish
Article numbere0160548
JournalPloS one
Volume11
Issue number8
DOIs
Publication statusPublished - Aug 1 2016

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Least-Squares Analysis
mitogen-activated protein kinase
least squares
Molecules
Immediate-Early Genes
Genes
Time series
Signal transduction
time series analysis
Gene expression
Data structures
Nonlinear systems
Phosphotransferases
genes
Reproduction
signal transduction
Signal Transduction
Processing
Gene Expression
gene expression

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

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Laguerre filter analysis with partial least square regression reveals a priming effect of ERK and CREB on c-FOS induction. / Kudo, Takamasa; Uda, Shinsuke; Tsuchiya, Takaho; Wada, Takumi; Karasawa, Yasuaki; Fujii, Masashi; Saito, Takeshi H.; Kuroda, Shinya.

In: PloS one, Vol. 11, No. 8, e0160548, 01.08.2016.

Research output: Contribution to journalArticle

Kudo, Takamasa ; Uda, Shinsuke ; Tsuchiya, Takaho ; Wada, Takumi ; Karasawa, Yasuaki ; Fujii, Masashi ; Saito, Takeshi H. ; Kuroda, Shinya. / Laguerre filter analysis with partial least square regression reveals a priming effect of ERK and CREB on c-FOS induction. In: PloS one. 2016 ; Vol. 11, No. 8.
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