Research article
Circadian signatures in rat liver: from gene expression to pathways
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* Corresponding author: Ioannis P Androulakis yannis@rci.rutgers.edu
1 Chemical and Biochemical Engineering Department, Rutgers University Piscataway, NJ 08854, USA
2 Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA
3 Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA
4 Biomedical Engineering Department, Rutgers University Piscataway, NJ 08854, USA
BMC Bioinformatics 2010, 11:540 doi:10.1186/1471-2105-11-540
Published: 1 November 2010Additional files
Additional file 1:
The relative values of the associated eigenvalues for glycine, serine and threonine metabolism. The bars indicate the variation in the data captured by each individual eigenvector for glycine, serine and threonine metabolism pathways. T solid line represents the data variability captured by the corresponding eigenvectors when randomly generated data (of the same dimension) were used. No apparent distinction between the actual data and randomly generated data was identified after the first eigenvalue, as quantified by the calculated p-values.
Format: JPEG Size: 643KB Download file
Additional file 2:
The first 4 rows of 
that are retrieved from SVD calculations of Glycine, serine and threonine metabolism
the elements of SP (k, t) are sorted from the highest to the lowest. 1)
2) 
3) 
4)
Format: JPEG Size: 1.2MB Download file
Additional file 3:
Pathway activity levels of five clusters and associated information of the genes in pathways. The excel file contains two sheets. First sheet, Pathway Activities includes the pathway activity levels and associated cluster numbers. Second Sheet contains the genes in selected pathways and associated information such as gene expression, weights and correlations.
Format: XLSX Size: 4.3MB Download file
Additional file 4:
Enriched pathways by circadian genes. The circadian genes were mapped to canonical pathways provided by http://www.broadinstitute.org/gsea/msigdb/ webcite. p-values indicate the significance of the overlap of the circadian genes within a pathway
Format: XLSX Size: 12KB Download file
Additional file 5:
Individual gene expressions in cholesterol biosynthesis. Associated weights and correlations with the fitted sinusoidal model were given on top of each panel.
Format: PNG Size: 294KB Download file
Additional file 6:
Individual gene expressions in bile acid biosynthesis. Associated weights and correlations with the fitted sinusoidal model were given on top of each panel.
Format: PNG Size: 283KB Download file
