Table 1 Gene co-expression network construction steps (a) five genes with their expression values (b) co-relation matrix showing correlation among five genes (c) network adjacency matrix where correlation above threshold (> 0.5) is presented as ‘1’, otherwise it is ‘0’
(a) Genes with the expression values | Sample ID\Gene ID | Gene expression values | ||||
cg25226014 (Gene 1) | cg00176210 (Gene 2) | cg04369341 (Gene 3) | cg00936626 (Gene 4) | cg01354473 (Gene 5) | ||
TCGA.02.0047.01A | 0.85 | 0.82 | 0.70 | 0.82 | 0.84 | |
TCGA.02.0055.01A | 0.57 | 0.69 | 0.17 | 0.89 | 0.56 | |
TCGA.02.2483.01A | 0.91 | 0.87 | 0.83 | 0.86 | 0.84 | |
TCGA.02.2485.01A | 0.91 | 0.90 | 0.41 | 0.90 | 0.75 | |
TCGA.02.2486.01A | 0.84 | 0.64 | 0.65 | 0.49 | 0.70 | |
(b) Co-relation matrix | Gene ID | Correlation values | ||||
cg25226014 (Gene 1) | cg00176210 (Gene 2) | cg04369341 (Gene 3) | cg00936626 (Gene 4) | cg01354473 (Gene 5) | ||
cg25226014 (Gene 1) | 1.00 | 0.15 | 0.23 | -0.01 | 0.06 | |
cg00176210 (Gene 2) | 0.15 | 1.00 | 0.55 | 0.54 | 0.42 | |
cg04369341 (Gene 3) | 0.23 | 0.55 | 1.00 | 0.50 | 0.51 | |
cg00936626 (Gene 4) | -0.01 | 0.54 | 0.50 | 1.00 | 0.30 | |
cg01354473 (Gene 5) | 0.06 | 0.42 | 0.51 | 0.30 | 1.00 | |
(c) Network adjacency matrix | Gene ID | Significant correlation indicated as ‘1’ | ||||
cg25226014 (Gene 1) | cg00176210 (Gene 2) | cg04369341 (Gene 3) | cg00936626 (Gene 4) | cg01354473 (Gene 5) | ||
cg25226014 (Gene 1) | 1 | 0 | 0 | 0 | 0 | |
cg00176210 (Gene 2) | 0 | 1 | 1 | 1 | 0 | |
cg04369341 (Gene 3) | 0 | 1 | 1 | 1 | 1 | |
cg00936626 (Gene 4) | 0 | 1 | 1 | 1 | 0 | |
cg01354473 (Gene 5) | 0 | 0 | 1 | 0 | 1 | |