Aliphatic glucosinolate is an important secondary metabolite responsible in plant defense mechanism and carcinogenic
activity. It plays a crucial role in plant adaptation towards changes in the environment such as salinity and drought.
However, in many plant genomes, there are thousands of genes encoding proteins still with putative functions and
incomplete annotations. Therefore, the genome of Arabidopsis thaliana was selected to be investigated further to identify
any putative genes that are potentially involved in the aliphatic glucosinolate biosynthesis pathway, most of its gene are
with incomplete annotation. Known genes for aliphatic glucosinolates were retrieved from KEGG and AraCyc databases.
Three co-expression databases i.e., ATTED-II, GeneMANIA and STRING were used to perform the co-expression network
analysis. The integrated co-expression network was then being clustered, annotated and visualized using Cytoscape plugin,
MCODE and ClueGO. Then, the regulatory network of A. thaliana from AtRegNet was mapped onto the co-expression
network to build the transcriptional regulatory network. This study showed that a total of 506 genes were co-expressed
with the 61 aliphatic glucosinolate biosynthesis genes. Five transcription factors have been predicted to be involved
in the biosynthetic pathway of aliphatic glucosinolate, namely SEPALLATA 3 (SEP3), PHYTOCHROME INTERACTING FACTOR
3-like 5 (AtbHLH15/PIL5), ELONGATED HYPOCOTYL 5 (HY5), AGAMOUS-like 15 (AGL15) and GLABRA 3 (GL3). Meanwhile,
three other genes with high potential to be involved in the aliphatic glucosinolates biosynthetic pathway were identified,
i.e., methylthioalkylmalate-like synthase 4 (MAML-4) and aspartate aminotransferase (ASP1 and ASP4). These findings
can be used to complete the aliphatic glucosinolate biosynthetic pathway in A. thaliana and to update the information
on the glucosinolate-related pathways in public metabolic databases.