Pseudomonas aeruginosa is
an opportunistic gram-negative bacterial pathogen that infects immune-compromised individuals, and causes persistent respiratory infections in cystic fibrosis (CF) patients. It also shows high resistance to many antibiotics. Hence, P. aeruginosa has been major model bacterium to study molecular mechanisms of opportunistic pathogenesis and antibiotic resistance. Various forward- and reverse-genetics approaches have been applied to identify drug targets (bacterial-specific essential genes) and intrinsic drug resistance genes (i.e., intrinsic resistome). Despite all these efforts, we have seen increasing failure rate of antibiotics treatments against P. aeruginosa during the past decade. Therefore, we might need complementary approaches to deeper understanding of pathogenesis and drug resistance of P. aeruginosa.

PseudomonasNet is
a database of genome-wide co-functional network for P. aeruginosa. By integration of 9 distinct types of data, PseudomonasNet covers more than 98% of the 5,572 coding genes of PAO1 strain with 203,118 co-functional links.

Web tools
for generating functional hypothesis about genes and functions of P. aeruginosa are also provided by running various network algorithms on PseudomonasNet. First, 'Pathway-centric search' search option prioritizes candidate genes for a pathway or phenotype. Second, 'Gene-centric search' prioritizes candidate functions for a P. aeruginosa gene. Due to the poor functional annotations for P. aeruginosa genes, we also provide functional annotations of E. coli orthologs. Last, PseudomonasNet web server provides context-centric predictions, 'Context-centric search '. Here, the server contains pre-defined set of genes which are PseudomonasNet neighbors of each P. aeruginosa genes. The hub of each subnetwork is considered as a modulator of its neighbors. Users submit differentially expressed genes (DEGs) upon cell state transition (e.g., drug response). Then the server measure statistical association between the cell-state associated DEGs and PseudomonasNet neighbors of each P. aeruginosa gene. Association between them suggests that the hub gene is candidate modulator of the cell-state.

How to cite PseudomonasNet
Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa. Sci Rep. 2016 May 19;6:26223. doi: 10.1038/srep26223.

Contact information
Insuk Lee (insuklee (at)

This work was supported by the National Research Foundation of Korea grant (2012M3A9B4028641, 2012M3A9C7050151).