Temporal and spatial patterns of gene profiles during chondrogenic differentiation

Clustering analysis based on temporal profile of genes may provide new insights in particular biological processes or conditions. We report such an integrative clustering analysis which is based on the expression patterns but is also influenced by temporal changes. The proposed platform is illustrated with a temporal gene expression dataset comprised of pellet culture-conditioned human primary chondrocytes and human bone marrow-derived mesenchymal stem cells (MSCs). We derived three clusters in each cell type and compared the content of these classes in terms of temporal changes. We further considered the induced biological processes and the gene-interaction networks formed within each cluster and discuss their biological significance. Our proposed methodology provides a consistent tool that facilitates both the statistical and biological validation of temporal profiles through spatial gene network profiles.