Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers

BACKGROUND: Although prognostic biomarkers specific for particular cancers have been discovered, microarray analysis of gene expression profiles, supported by integrative analysis algorithms, helps to identify common factors in molecular oncology. Similarities of Ordered Gene Lists (SOGL) is a recently proposed approach to meta-analysis suitable for identifying features shared by two data sets. Here we extend the idea of SOGL to the detection of significant prognostic marker genes from microarrays of multiple data sets. Three data sets for leukemia and the other six for different solid tumors are used to demonstrate our method, using established statistical techniques. RESULTS: We describe a set of significantly similar ordered gene lists, representing outcome comparisons for distinct types of cancer. This kind of similarity could improve the diagnostic accuracies of individual studies when SOGL is incorporated into the support vector machine algorithm. In particular, we investigate the similarities among three ordered gene lists pertaining to mesothelioma survival, prostate recurrence and glioma survival. The similarity-driving genes are related to the outcomes of patients with lung cancer with a hazard ratio of 4.47 (p = 0.035). Many of these genes are involved in breakdown of EMC proteins regulating angiogenesis, and may be used for further research on prognostic markers and molecular targets of gene therapy for cancers. CONCLUSION: The proposed method and its application show the potential of such meta-analyses in clinical studies of gene expression profiles

Effect of chlorhexidine (0.12%) rinses on periodontal tissue healing after tooth extraction. (II). Radiographic parameters.

The aim of the present study was to assess the influence of a 1-month period of chlorhexidine digluconate (CHX) rinses on the remodelling activity of periodontal tissues adjacent to an extraction wound. From 12 patients assigned to the test group rinsing 2 x daily with 15 ml of 0.12% CHX solution (Peridex) starting 2 days after tooth extraction and from 11 patients assigned to the control group rinsing with a placebo solution, standardized radiographs were available taken immediately after tooth extraction and 1, 2, 3 and 6 months thereafter. Computer assisted densitometric image analysis (CADIA) was applied in order to quantify changes in density during the healing phase after tooth extraction. Regions of interest (ROI) were chosen for CADIA covering supracrestal periodontal soft tissue adjacent to the extraction wound. ROIs were also defined on crestal alveolar bone adjacent to the extraction wound. In the active group, 15/20 sites demonstrated an increase in alveolar bone density between months 1 and 6 (mean CADIA value 6.7 +/- 10.0), whereas in the control group 11/21 sites demonstrated a loss in density (mean CADIA values -1.4 +/- 10.5). Similar observations were made when the ROIs covering supracrestal periodontal tissues were analyzed (mean CADIA values 7.8 +/- 8.4 for the experimental group and -0.3 +/- 10.5 for the control group). These differences were statistically significant (p < 0.04). The digitized series of standardized radiographs were also evaluated for changes in bone height. The distance from the alveolar bone crest to reference points were measured in mm within the baseline: the 1, 2, 3 and 6 month radiographs.(ABSTRACT TRUNCATED AT 250 WORDS)link_to_subscribed_fulltex