Dataset Information

Laguerre Filter Analysis with Partial Least Square Regression Reveals a Priming Effect of ERK and CREB on c-FOS Induction.

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.

SUBMITTER: Kudo T

PROVIDER: S-EPMC4981404 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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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 T Uda Shinsuke S Tsuchiya Takaho T Wada Takumi T Karasawa Yasuaki Y Fujii Masashi M Saito Takeshi H TH Kuroda Shinya S

PloS one 20160811 8

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 nonline ...[more]

PMID: 27513954

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Project description:In order to help reduce silicosis in miners, the National Institute for Occupational Health and Safety (NIOSH) is developing field-portable methods for measuring airborne respirable crystalline silica (RCS), specifically the polymorph α-quartz, in mine dusts. In this study we demonstrate the feasibility of end-of-shift measurement of α-quartz using a direct-on-filter (DoF) method to analyze coal mine dust samples deposited onto polyvinyl chloride filters. The DoF method is potentially amenable for on-site analyses, but deviates from the current regulatory determination of RCS for coal mines by eliminating two sample preparation steps: ashing the sampling filter and redepositing the ash prior to quantification by Fourier transform infrared (FT-IR) spectrometry. In this study, the FT-IR spectra of 66 coal dust samples from active mines were used, and the RCS was quantified by using: (1) an ordinary least squares (OLS) calibration approach that utilizes standard silica material as done in the Mine Safety and Health Administration's P7 method; and (2) a partial least squares (PLS) regression approach. Both were capable of accounting for kaolinite, which can confound the IR analysis of silica. The OLS method utilized analytical standards for silica calibration and kaolin correction, resulting in a good linear correlation with P7 results and minimal bias but with the accuracy limited by the presence of kaolinite. The PLS approach also produced predictions well-correlated to the P7 method, as well as better accuracy in RCS prediction, and no bias due to variable kaolinite mass. Besides decreased sensitivity to mineral or substrate confounders, PLS has the advantage that the analyst is not required to correct for the presence of kaolinite or background interferences related to the substrate, making the method potentially viable for automated RCS prediction in the field. This study demonstrated the efficacy of FT-IR transmission spectrometry for silica determination in coal mine dusts, using both OLS and PLS analyses, when kaolinite was present.

Dataset Information

Laguerre Filter Analysis with Partial Least Square Regression Reveals a Priming Effect of ERK and CREB on c-FOS Induction.

Publications

Laguerre Filter Analysis with Partial Least Square Regression Reveals a Priming Effect of ERK and CREB on c-FOS Induction.

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