Figure 1
Heat map representation of differentially expressed genes belonging to the “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. Arbitrary signal intensity acquired from microarray analysis is represented by colours (green, higher; red, lower expression). Log2 signal intensity values for any single gene were resized to Row Z-Score scale (from -2, the lowest expression to +2, the highest expression for single gene). The 20 genes selected to this publication was marked green for upregulation and red for downregulation
Table.1
Gene symbols, fold change in expression ratio, Entrez gene IDs, corrected p values and mean value of fold change ratio of the 20 chosen differentially expressed, studied genes
| GENE SYMBOL | RATIO D7/D1 | RATIO D30/D1 | RATIO D15/D1 | ADJUSTED P.VALUE D7/D1 | ADJUSTED P.VALUE D15/D1 | ADJUSTED P.VALUE D30/D1 | ENTREZ GENE ID | MEAN RATIO |
|---|---|---|---|---|---|---|---|---|
| OASL | -19.013577 | -19.59127971 | -20.33618335 | 2.69E-05 | 1.34E-05 | 7.93E-06 | 595119 | -19.64701335 |
| PIM1 | -2.278169547 | -7.702016846 | -14.75410523 | 0.000841907 | 7.24E-06 | 1.14E-06 | 100157844 | -8.244763875 |
| RAB27A | -2.438418171 | -6.421074057 | -12.17306946 | 0.000240688 | 4.70E-06 | 7.36E-07 | 606749 | -7.010853897 |
| ERBB3 | -3.700854877 | -8.072357208 | -8.474685238 | 4.67E-05 | 3.53E-06 | 1.48E-06 | --- | -6.749299107 |
| DDX60 | -9.539122077 | -5.148779 | -4.690032007 | 7.61E-05 | 0.000244171 | 0.000232065 | --- | -6.459311028 |
| NAV3 | -2.570715662 | -3.817701681 | -12.08344185 | 0.005032343 | 0.000725275 | 2.01E-05 | --- | -6.157286398 |
| MX2 | -8.476906188 | -5.025767174 | -2.864164098 | 3.11E-05 | 6.87E-05 | 0.000433456 | 396893 | -5.455612486 |
| MCM4 | -1.824811573 | -2.553654794 | -11.20276401 | 0.001672766 | 0.000140647 | 8.81E-07 | 100156398 | -5.193743459 |
| DHX58 | -6.093081701 | -5.06259312 | -3.519635478 | 2.24E-05 | 1.83E-05 | 4.23E-05 | 100524520 | -4.891770099 |
| OAS1 | -4.734227264 | -4.803325858 | -4.579644931 | 0.000637714 | 0.000454579 | 0.00038381 | --- | -4.705732684 |
| CFTR | 5.930096417 | 5.971243553 | 3.580726141 | 4.73E-05 | 2.79E-05 | 0.000103206 | 403154 | 5.160688703 |
| BVES | 5.084835235 | 6.889451287 | 4.958469165 | 0.000164789 | 4.63E-05 | 7.99E-05 | 100153106 | 5.644251896 |
| NUAK1 | 5.90004438 | 7.687798942 | 4.205418788 | 2.17E-05 | 5.48E-06 | 1.88E-05 | 100523669 | 5.93108737 |
| PANK1 | 7.855561899 | 3.491673705 | 7.158649931 | 7.45E-06 | 3.27E-05 | 2.08E-06 | 100154650 | 6.168628512 |
| ACAA2 | 4.821347296 | 6.223974104 | 7.791004625 | 1.04E-05 | 3.05E-06 | 8.03E-07 | 100312959 | 6.278775342 |
| FGFR1 | 4.599714105 | 5.650775055 | 8.942976069 | 1.33E-05 | 3.63E-06 | 6.88E-07 | 100153248 | 6.397821743 |
| P2RX7 | 6.165142343 | 8.522042354 | 5.795397835 | 2.69E-05 | 6.72E-06 | 1.03E-05 | 497623 | 6.827527511 |
| KIF23 | 6.496859984 | 7.105965066 | 7.104751913 | 0.000646977 | 0.000381978 | 0.000271214 | 100522116 | 6.902525654 |
| ABCA1 | 6.313396076 | 5.556746901 | 10.33557918 | 3.95E-05 | 3.12E-05 | 4.36E-06 | 100152112 | 7.401907384 |
| ACTA2 | 5.225241405 | 12.54084054 | 30.24621828 | 3.15E-05 | 3.09E-06 | 4.37E-07 | 733615 | 16.00410008 |
Figure 2
The circle plot showing the differently expressed genes and z-score of the “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The outer circle shows a scatter plot for each term of the fold change of the assigned genes. Green circles display upregulation and red ones downregulation. The inner circle shows the z-score of each GO BP term. The width of the each bar corresponds to the number of genes within GO BP term and the color corresponds to the z-score
Figure 3
The representation of the mutual relationship of differently expressed genes that belongs to 20 chosen genes from “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The ribbons indicate which gene belongs to which categories. The middle circle represents logarithm from fold change (LogFC) between D7/D1, D15/D1 and D30/D1 respectively. The color of each block corresponds to the LogFC of each gene (green – upregulated, red – downregulated). The genes were sorted by logFC from most to least changed gene
Figure 4
Heatmap showing the gene occurrence between chosen 20 differently expressed genes that belongs to “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The yellow color is associated with gene occurrence in the GO Term. The intensity of the color is corresponding to amount of GO BP terms that each gene belongs to
Figure 5
STRING-generated interaction occurrence between 20 chosen differently expressed genes that belong to the “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding” GO BP terms. The intensity of the edges reflects the strength of interaction score