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.


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.

List of Tables

Gene Set Level Network

We constructed a gene set level network in order to obtain a systems level perspective of the results. Each node in this network is an up-regulated gene set and two gene sets are connected by an edge if they share a statistically significant number of genes. We have included only those connections between gene sets that are significant after correcting for testing multiple hypotheses using the method of Benjamini and Hochberg. We placed a gene set at the first time point at which it was significantly up-regulated (i.e., had a q-value reported by GSEA of at most 0.2).