Transcriptome analysis of common gene expression in human mesenchymal stem cells derived from four different origins

We have used Affymetrix oligonucleotide microarrays to analyze common transcriptomes and thereby learn about the core gene expression profile in human mesenchymal stem cells (MSC) from different tissues, including fetal amniotic fluid-derived MSC, term pregnancy amniotic membrane-derived MSC, term pregnancy umbilical cord blood-derived MSC, and adult bone marrow-derived MSC. The beauty of microarray analysis of gene expression (MAGE) is that it can be used to discover associating genes that were previously thought to be unrelated to a physiological or pathological event. However, interpreting complex biological processes from gene expression profiles often requires extensive knowledge mining in biomedical literature. In this chapter, we describe, step-by-step, how to use a commercially available biological database and software program, MetaCore (GeneGo Inc.), for functional network analysis.