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Open Access Open Badges Research article

Frequency-based time-series gene expression recomposition using PRIISM

Bruce A Rosa12, Yuhua Jiao2, Sookyung Oh2, Beronda L Montgomery23, Wensheng Qin1* and Jin Chen24*

Author Affiliations

1 Biorefining Research Initiative and Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON, P7B 5E1, Canada

2 MSU-DOE Plant Research Laboratory, Plant Biology Laboratories, Michigan State University, 612 Wilson Road, Rm. 106, East Lansing, MI, 48824, USA

3 Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, East Lansing, MI, 48824, USA

4 Department of Computer Sciences and Engineering, Michigan State University, 3115 Engineering Building, East Lansing, MI, 48824, USA

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BMC Systems Biology 2012, 6:69  doi:10.1186/1752-0509-6-69

Published: 15 June 2012

Additional files

Additional file 1:

Figure S1: Time frames used to generate FFT results. Frame sizes and positions are shown in (A) and the contribution of each frame to the weighted average at each timepoint is shown in (B). Figure S2: Principal Component Analysis (PCA) Plots. Principal component analysis (PCA) plots for the original data (A) and the first components of the clock-frequency and treatment-frequency data (B) are shown. COS-upregulated genes are shown in black circles, COS-downregulated genes (which are not analyzed in detail here) are shown in white diamonds and all other genes are shown as grey dots. Figure S3: The original, mean-shifted, PRIISM-reconstructed and Butterworth-filter reconstructed gene expression patterns ofAtGolS3. (A) The original (black) and mean-shifted (grey) expression values of AtGolS3. (B) Comparison between the treatment-frequency-reconstructed gene expression patterns for AtGolS3 using PRIISM (Black line) and using a fifth-order Butterworth low-pass filter (grey line). Figure S4: The frequency spectra of the original, the PRIISM-reconstructed and the Butterworth-filter reconstructed gene expression patterns ofAtGolS3. (A) The Frequency Spectrum of the original gene expression pattern of AtGolS3. (B) Comparison of the frequency spectra of AtGolS3 after processing using PRIISM (white circles) and the fifth-order Butterworth low-pass filter (grey diamonds). The original treatment-frequency spectrum of AtGolS3 is also shown (red bars). Figure S5: The Bode plot of a fifth-order Butterworth low-pass filter forAtGolS3.

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