In the context of the cell cycle, matrix stiffness has been identified as a key regulator of entry into S phase (Klein et al., 2009; Wang et al., 2000).
On the other hand, before completing 300 freezing and thawing cycles, matrix (ECC without fiber) specimens have severely deteriorated, requiring removal from the freeze thaw machine.
From this perspective, the large nodes are clustered together, particularly in the cell cycle, extracellular matrix and glycolysis modules.
Using a genome-wide gene expression analysis we found alterations in genes belonging to specific categories (cell cycle, extracellular matrix (ECM) and fibrosis, cellular architecture/motility and apoptosis).
Each cell or tile agent then performs biological rules specific to its own position in the cell cycle or matrix remodeling process.
We were able to classify differentially expressed genes in ALMS fibroblasts into 4 groups: cell cycle, extracellular matrix components/fibrosis regulation, cellular adhesion/motility and apoptosis (Figure 2, Table 2 and Table S2).
Taking into account GO term and intra-connectivity, the major functional modules contain an enrichment of cell cycle, extracellular matrix, glycolysis/fast twitch muscle subunits, slow twitch muscle subunits, nuclear-encoded mitochondrial and mitochondrially-encoded mitochondrial genes.
The cycle between matrix degradation and chondrocyte loss ultimately results in gross changes in cartilage characteristics of OA.
Generally, we observed a down-regulation of gene sets encoding for cell cycle, extracellular matrix and translation [ 20].
