The latest version of SameSpots software for 2D gel electrophoresis analysis of differential expression has not only a new look, but also includes a new workflow.
Since the creation of SameSpots in 2004, the software was developed to be easy-to-use and reproducible for differential expression analysis.
The latest release in October has maintained the ease of use and the reproducibility of the software was demonstrated in internal tests with results presented by poster at a recent conference.
New features added to the analysis included the additional experimental design – two-way ANOVA. Previously there had been two experimental designs – 1. between subject, to analyse differences between two distinct conditions, and 2. within subject design to analyse differences between conditions within a subject. The addition of two-way ANOVA allows for analysis of two sets of conditions, commonly used to investigate the effects of a given condition on wild-type and mutant strains or species.
The inclusion of the two-way ANOVA calculation required an update to the multivariate statistics screen. In addition to ANOVA tables, it is now easier to access the existing statistics including, q-values, principle component analysis (PCA), correlation analysis, power analysis and expression profiles.
Exporting results remains similar; raw data, tables and all images can be exported as .csv data files or through the clip gallery tool in high quality for presentations and reports. The production of an HTML report now includes the opportunity to include a text annotation.
The reproducibility of the software was assessed internally by 4 users, ranging from expert to novice.
Each user analysed the same set of DIGE images and identified all spots which showed a statistically significant change (ANOVA p-value ≤ 0.05) and a fold change ≥ 1.5 between the two conditions. Users identified up to 95% of the same spots as one another and the ranking of these spots (from smallest ANOVA p-value to 0.05) was similar between users.
Overall the key benefits of SameSpots which are that it is quick, easy-to-use and provides reproducible results have been maintained with added benefits of more accessible and additional analysis features.
