Predicting disease genes using protein-protein interactions

Discovering disease-genes by topological features in human protein-protein interaction network

MOTIVATION

Mining the hereditary disease-genes from human genome is one of the most important tasks in bioinformatics research. A variety of sequence features and functional similarities between known human hereditary disease-genes and those not known to be involved in disease have been systematically examined and efficient classifiers have been constructed based on the identified common patterns. The availability of human genome-wide protein-protein interactions (PPIs) provides us with new opportunity for discovering hereditary disease-genes by topological features in PPIs network.

RESULTS

This analysis reveals that the hereditary disease-genes ascertained from OMIM in the literature-curated (LC) PPIs network are characterized by a larger degree, tendency to interact with other disease-genes, more common neighbors and quick communication to each other whereas those properties could not be detected from the network identified from high-throughput yeast two-hybrid mapping approach (EXP) and predicted interactions (PDT) PPIs network. KNN classifier based on those features was created and on average gained overall prediction accuracy of 0.76 in cross-validation test. Then the classifier was applied to 5262 genes on human genome and predicted 178 novel disease-genes. Some of the predictions have been validated by biological experiments.

In-vitro study of the activity of ciprofloxacin alone and in combination against strains of Pseudomonas aeruginosa with multiple antibiotic resistance

Ciprofloxacin appears to have useful activity against Pseudomonas aeruginosa. We have studied its in-vitro activity against ten strains of Ps. aeruginosa with multiple antibiotic resistance. We have confirmed that ciprofloxacin is very active against Ps. aeruginosa with minimal inhibitory concentrations ranging from 0.07 to 0.7 mg/l. Killing curves show ciprofloxacin to be rapidly bactericidal with no regrowth after 24 h. Checkerboard studies with ciprofloxacin in combination with gentamicin, azlocillin and ceftazidime show no consistent interaction. These studies suggest that ciprofloxacin should prove a useful antibiotic in treating infections caused by multiresistant Ps. aeruginosa.