Supplementary data for A Comparative Study of Genome Wide Transcriptional Profiles of Primary Hepatocytes in Collagen Sandwich and Monolayer Cultures
Y. Kim, C. D. Lasher, L. M. Milford, T. M. Murali, and P. Rajagopalan

Expression Data

Gene expression data is available at the Gene Expression Omnibus (GEO). The accession id is GSE20659.

Tables

The following tables present results from Gene Set Enrichment Analysis (GSEA). Below we present a brief explanation and tips to help interpret and use the tables.

• Each row represents evaluations for a gene set, for example, "glycine and serine metabolism".
• Each column represents a contrast evaluated by GSEA for enrichment.
• Each cell contains a q-value.

  The value in each cell represents the statistical significance of the perturbation of the gene set in that row for the contrast in that column. The value is the q-value, which is a measure of the False Discovery Rate (FDR). q-values closer to zero represent greater perturbation of the gene set. See the GSEA User Guide for more details.

  While q-values are always positive (and lie between 0 and 1), we augment them with a sign (positive or negative). The sign of a q-value indicates whether the gene set was mainly up-regulated (positive values) or down-regulated (negative values) in the first phenotype in the contrast when compared to the second phenotype in the contrast. For example, for a contrast "Double-gel vs. Single-gel at 48 hours", a signed q-value of -4e-03 for "Cell Cycle" indicates that this gene set was down-regulated overall for the double-gel culture when compared against the single-gel culture.

• Calculations resulting in q-values > 0.2 (or < -0.2) were converted to 1 (or -1) to indicate insignificant evidence of perturbation.
• Hover the mouse pointer over a cell to display the q-value to a greater precision.

List of Tables

• Table of all q-values from GSEA comparisons

  Note: some cells include links to further details for a specific gene set in a respective comparison; clicking the links takes the user to these details.

  Note: The colour scheme used in these tables is RdYlGn from Color Brewer.

• Text (CSV) table of all q-values from GSEA comparisons

  Use this file to view the comparisons as a spreadsheet in OpenOffice.org Calc, Microsoft Excel, or similar program.

• Selected downregulated gene sets
• Selected upregulated gene sets

Gene Set Level Network