GeneSpring microarray analysis software is seen as the industry standard for microarray analysis. GeneSpring aims to bring together all the steps of microarray data analysis in one single software package. Whether used for comparative genomics studies or expression studies, GeneSpring contains enough components and options to allow users to perform a detailed analysis using their microarray data.
The current version of GeneSpring GX is 11.5. GeneSpring uses files generated from an image quantification software where intensity values were assigned to each spot. It contains a unique graphical user interface where data sets are contained within folders and a graphical representation of the genome can be displayed simultaneously. Genome files are required to set up the genome represented on the microarray and to allow a suitable gene list to be created that is representative of the genome. Once this has been created and installed, quantified data files can be used to create experiments. It is at this point that various settings are selected such as the type of normalization to be used on the data, whether to create linear and/or log replicates and importantly, to create parameters and select parameters. These selections are critical for the correct interpretation of the data.
Comparative genomics requires the selection of present genes and genes that are 'absent or highly divergent'. Once the experiment has been set up it is possible to carry out quality control of genes to eliminate flagged genes and also to filter out genes based on statistical analysis. Filtering is a key process in which statistical methods are used to show whether genes in a certain group can be proved to be significant or not i.e. by carrying out t-tests. Additional techniques such as clustering can also be carried out along with the ability to input new software written in different languages e.g. Java.
Microarray experiments come to a completion with the analysis of data. GeneSpring software offers the chance to carry out many of these steps using a single package.
To view a basic protocol for GeneSpring, click here.
To view frequently asked questions on GeneSpring, click here.