The overlap of Set 1 contains only four genes, but two of these are fast muscle myosin genes, myl1 and mylpfa (Fig. 7A; supplementary material Table S3).
However, the overlap of Set 3 also contains fast muscle genes, such as atp1a2a, myom1a and srl (Fig. 7C; supplementary material Table S3).
The overlap of Set 2 contains fast muscle differentiation genes, including atp2a1, a fast muscle SERCA Ca(2+ -ATPase (Wu et al., 1995), ryr1b (Hirata et al., 2+ -ATPase also myog (Fig. 7B; supplementary material Table S3).
Venn diagram calculations were performed in Visual Basic code for MS Excel 2000 to analyze overlapping of sets of genes differentially expressed in the samples at different phases of arthritis.
The index provides a measure of the overlap of two sets.
The studies of Komashko et al. also showed a very low overlap of the sets of promoters having high levels of H3K9me3 versus high levels of DNA methylation.
For example, PI association between genes a and b measures the significance of the overlap of two sets.
In their study Agam et al. [ 17] referred to the overlap of two sets of CNA between technical replicates.
The fuzzy set for α j =0.5 and α j =1.0 (Fig. 6 b) provides more information as offering smaller overlap of the sets.
Furthermore, network biology focuses on the importance of clusters [ 58- 61] as a measure of similarity rather than simply an overlap of gene sets.
