Table 3.
TimeDelay-ARACNE test on the yeast eleven genes network.
| Genes | Kegg | Correct | Wrong |
|---|---|---|---|
| Cln3 | Swi4, Swi6, Mbp1 | Swi4, Swi6, Mbp1 | - |
| Swi6 | Cln1/2, Clb5/6 | Cln1, Clb6 | Clb5 |
| Swi4 | Cln1/2, CDC28 | Cln1 | Clb6 |
| Mbp1 | Clb5/6, Cdc28 | - | - |
| Cln1 | Sic1 | Sic1 | - |
| Cln2 | Sic1, Swi4/6 | Sic1, Swi4 | - |
| Clb5 | Cdc6 | - | Sic1 |
| Clb6 | Cdc6 | Cdc6 | - |
| Sic1 | Clb5/6, Cdc28 | - | - |
| Cdc6 | - | - | Sic1 |
| Cdc28 | Swi4/6, Mbp1, Cln1/2, Sic1, Cdc6 | Swi6, Mbp1 | Clb5 |
It is important to underline that Cdc28 is the only yeast Cyclin-dependent kinase and it is present during the whole cell cycle. From the KEGG pathway it is clear that Cdc28 makes complex with cyclins (Cln and Clb) but these complexes are of course at proteomic level and they aren't related to the Cdc28 transcription but mostly to the cyclins transcript levels. According to this, TimeDelay-ARACNE misconnections couldn't be considered errors.