TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

BMC Bioinformatics

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.

ISSN: 1471-2105