Performing Pathway Analysis Downstream of AltAnalyze
After running AltAnalyze to identify differentially or alternatively expressed genes, it is recommended that the users explore these results along biological pathways. Within AltAnalyze users can select the GO-Elite option to obtain over-representation results for a number of ontologies, pathway and gene-set databases. In addition, the input files created for GO-Elite (GO-Elite/input directory) can be used to directly visualize gene expression or alternative exon results on WikiPathways, using the AltAnalyze interface Additional Analyses and Pathway Visualization. Since this interface has limited options for pathway visualization, the user may want to use more sophisticated pathway visualization programs. Two examples are listed below.
To load the GenMAPP input text file produced by AltAnalyze (ExpressionOutput directory), see the following tutorials.
PathVisio, like GenMAPP-CS, can be used to load pathways from WikiPathways. In addition, it can create new pathways and has a number of sophisticated options for streamlined data visualization.
The same input file used for GenMAPP-CS can also be loaded into PathVisio. This will require that the text file is imported and processed before creating criterion. For example directions, see their tutorial here.