3.1. OSAnalyzer
OSAnalyzer is a platform-independent application and it is entirely implemented using the Java 6 programming language, making it available for Windows, Linux, and MacOSX operating systems.
OSAnalyzer provides a simple and essential graphical user interface (GUI) allowing the users easy access to the tool`s functionalities. OSAnalyzer is very simple to use, the analysis of a complete OS-dataset requires just some clicks with the mouse, which are: (i) load the input OS-dataset by using the command “File” located in the menu bar as shown in Figure 6a; as result, OSAnalyzer shows to the user a file system navigation windows; (ii) browse the file system, in order to select the file to analyze (see Figure 6b); and (iii) wait as the OSAnalyzer finishes the computation and shows the results sorted in descending order according to the statistical significance of the log-rank test, and conveyed in two separate navigation panel results, one for OS, and one for PFS.
The use of two different navigation panel results makes it simple to locate the most relevant results for OS and PFS. Thus, users can easily find out the significance of a probe with respect to the OS and PFS (see Figure 6c). The main goal of the navigation panel results is to simplify the analysis of the results. In fact, each meaningful probe is related with three curves obtained by comparing the detected alleles in pairs, which present different values of significance. Thus, using the search function (locate in the top right corner of the window), it is possible to see the value of each curve (log-rank test) obtained comparing the three groups among them, Figure 6c. Selecting one probe per time and using the buttons “plot-os” or “plot-pfs” it is possible to see OS or PFS curves as depicted in Figure 6d. Moreover, at the bottom of the window, OSAnalyzer provides a quick summary of the most important measures for survival curves comparison such medians and the hazard ratio for each curve, as shown in see Figure 6d. The user can save the results and the curves that he/she considers relevant on file, by clicking with the right button of the mouse on the chart. Finally, OSAnalyzer can automatically annotate the relevant SNPs related to the overall survival by using annotation libraries provided by Affimetrix, or retrieving further information from dbSNP and PharmaGKB databases. OS-Analyzer is distributed under Creative Commons License, is freely downloadable for academic and not-for-profit institutions at: https://sites.google.com/site/overallsurvivalanalyzer/.
The automatic analysis of the whole microarray dataset avoids wasting time on the manual analysis of all probes in order to figure out which probes are relevant from an overall survival or PFS point of view. Users who are exploiting this feature of OSAnalyzer can automatically analyze a whole DMET microarray dataset in one go without further effort, as opposed to other available tools where the user is forced to manually organize the analysis of the whole dataset each time, increasing the possibility of introducing mistakes. This way, OSAnalyzer allows the users to focus only on the analysis of the results.
The capabilities made available by OSAnalyzer are: Loading and Analysis of OS-datasets: OSAnalyzer is currently able to parse information encoded in xlsx format (file format defined by Excel) and CSV (comma-separated value) data files, as well as tab-delimited files. This way users may also prepare their own dataset, e.g., merging together samples coming from different experimental batches;Overall survival significance: OSAnalyzer automatically computes and visualizes the overall survival significance related with all probes, showing to the users the probes ranked by p-value significance;Progression-Free Survival significance: OSAnalyzer automatically computes and visualizes the progression-free survival significance related with all probes, showing to the users the probes ranked by p-value significance;Overall and Progression-Free survival curves visualizer: it is possible to display the survival curve related with a selected probe. Furthermore, the current version of OSAnalyzer provides the users with additional information for the median related with each curve, the log-rank p-value and the hazard-ratio value;