On methods for gene function scoring as a means of facilitating the interpretation of microarray results.

As gene annotation databases continue to evolve and improve, it has become feasible to incorporate the functional and pathway information about genes, available in these databases into the analysis of gene expression data, for a better understanding of the underlying mechanisms. A few methods have been proposed in the literature to formally convert individual gene results into gene function results. In this paper, we will compare the various methods, propose and examine some new ones, and offer a structured approach to incorporating gene function or pathway information into the analysis of expression data. We study the performance of the various methods and also compare them on real data, using a case study from the toxicogenomics area. Our results show that the approaches based on gene function scores yield a different, and functionally more interpretable, array of genes than methods that rely solely on individual gene scores. They also suggest that functional class scoring methods appear to perform better and more consistently than overrepresentation analysis and distributional score methods.

DNA microarrays of the complex human cytomegalovirus genome: profiling kinetic class with drug sensitivity of viral gene expression.

We describe, for the first time, the generation of a viral DNA chip for simultaneous expression measurements of nearly all known open reading frames (ORFs) in the largest member of the herpesvirus family, human cytomegalovirus (HCMV). In this study, an HCMV chip was fabricated and used to characterize the temporal class of viral gene expression. The viral chip is composed of microarrays of viral DNA prepared by robotic deposition of oligonucleotides on glass for ORFs in the HCMV genome. Viral gene expression was monitored by hybridization to the oligonucleotide microarrays with fluorescently labelled cDNAs prepared from mock-infected or infected human foreskin fibroblast cells. By using cycloheximide and ganciclovir to block de novo viral protein synthesis and viral DNA replication, respectively, the kinetic classes of array elements were classified. The expression profiles of known ORFs and many previously uncharacterized ORFs provided a temporal map of immediate-early (alpha), early (beta), early-late (gamma1), and late (gamma2) genes in the entire genome of HCMV. Sequence compositional analysis of the 5' noncoding DNA sequences of the temporal classes, performed by using algorithms that automatically search for defined and recurring motifs in unaligned sequences, indicated the presence of potential regulatory motifs for beta, gamma1, and gamma2 genes. In summary, these fabricated microarrays of viral DNA allow rapid and parallel analysis of gene expression at the whole viral genome level. The viral chip approach coupled with global biochemical and genetic strategies should greatly speed the functional analysis of established as well as newly discovered large viral genomes.

Comparison of efficacies of oral levofloxacin and oral ciprofloxacin in a rabbit model of a staphylococcal abscess.

Oral levofloxacin was compared to oral ciprofloxacin in a Staphylococcus aureus subcutaneous abscess model in rabbits. Rabbits were surgically prepared with subcutaneous wiffle balls (43 mm in diameter) and allowed to recover for 4 to 6 weeks. Rabbits were infected by direct injection into the capsule with S. aureus ATCC 29213 (5 x 10(5) CFU) and were allowed to remain infected for 8 days before the initiation of anti-infective treatment. Efficacy was determined by assessing the bacterial load within the capsule over a 10-day treatment period. In single-dose pharmacokinetic studies in infected rabbits, similar area under the concentration-time curve/MIC ratios were obtained in the plasma and abscess fluid for levofloxacin at 45 mg/kg of body weight and ciprofloxacin at 200 mg/kg of body weight. Similar efficacies were seen with levofloxacin at 45 mg/kg/day and ciprofloxacin 400 mg/kg/day by day 10. In this model, levofloxacin was significantly more efficacious than ciprofloxacin (P < 0.01).

Step-down trend tests for identifying the minimum effective dose.

Many authors, most recently Tamhane, Hochberg, and Dunnett (18), have studied the problem of determining the minimum effective dose in dose-response studies. Based on past research and on findings from their own extensive simulation study, which covered a wide range of balanced normal homoscedastic situations, Tamhane et al. recommended a procedure they called SD2L, since it exhibited good performance in almost all the situations they studied. This method is a step-down procedure with a simple linear contrast-based trend test at each step. In this paper, we demonstrate that replacing the linear contrast trend test by Bartholomew's test leads to a procedure, SD2B, that consistently outperforms SD2L. In addition to the balanced normal homoscedastic framework, the finite sample performance of these procedures is also explored under unbalanced and/or heteroscedastic conditions. A third procedure, SD2W, which replaces the linear contrast test by Welch's test, offers some improvement over SD2B in a few heteroscedastic situations. In many cases, the increase in efficiency of SD2B and SD2W over SD2L exceeds 10%.

Reference ranges for screening preclinical drug safety data.

Reference ranges are used in preclinical drug safety studies to screen experimental data for atypical values. The methods used most often to construct sample reference ranges are essentially large sample methods and may flag too few "atypical" values. It is better to generate finite sample reference ranges by modifying existing methods used for constructing tolerance intervals. We define validity and efficiency for reference ranges and discuss the validity and efficiency of the methods described. A finite sample distribution-free method emerges as the clear winner.

In vivo oral efficacy of levofloxacin for treatment of systemic Pseudomonas aeruginosa infections in a murine model of septicemia.

The in vivo efficacies of levofloxacin and ciprofloxacin in lethal, systemic Pseudomonas aeruginosa infections in mice were compared. MICs of levofloxacin and ciprofloxacin ranged from 0.5 to 2.0 micrograms/ml and from 0.12 to 1.0 microgram/ml respectively. Infecting doses ranged from 5.0 x 10(1) to 3.2 x 10(3) CFU per mouse, depending on the isolate. Test fluoroquinolones were administered orally at 1 h (single dose) or at 1 and 3 h (divided dose) postinfection, with 10 infected mice used for each of six concentrations of each fluoroquinolone tested (1 to 40 mg/kg of body weight) in each dosing regimen. Whether given in a single or a divided dose, the total daily dose was the same for each fluoroquinolone. For mice treated 1 h postinfection with levofloxacin and ciprofloxacin, the effective doses for 50% of the infected mice ranged from 2.09 to 13.80 mg/kg and from 2.34 to 11.22 mg/kg, respectively, and for those treated 1 and 3 h postinfection, the effective doses for 50% of the infected mice ranged from 3.71 to 16.98 mg/kg and from 2.95 to 13.18 mg/kg, respectively. Although the potency varied for both levofloxacin and ciprofloxacin among all strains of P. aeruginosa tested, there were small differences within the same strain for levofloxacin and ciprofloxacin when given in the same dosing regimen. Levofloxacin proved nearly as effective as ciprofloxacin against a systemic P. aeruginosa infection in mice.