PMC

PathwAX workflow. After the user submits an input query, a subnetwork containing all query genes and their neighbours are requested from the server. A second request looks up all pathways sharing at least one gene with the subnetwork. In the final call the browser gets the parameters of the randomized connections between the pathways and the query gene. Once the browser has obtained the subnetwork, pathways of interest and the randomized connection parameters, it calculates the crosstalk statistics and displays these in the browser.

PathwAX results for the 14 genes in the human gene set LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_UP in MSigDB (PLXNA3, PSRC1, DLGAP4, HN1, CDC25C, FLNB, C20ORF20, CCND1, ACOT7, FLJ20674, TGFB1I1, LOX, DDAH1, CDC42EP3). The upper table and pie diagram summarize the results and visualize the distribution of pathway classes. The lower table lists all enriched (blue) and depleted (red) pathways for the query that are significant for the chosen cutoff (only top part shown). The pathways may be restricted to a class by clicking on one in the upper table. The results are sorted by increasing FDR. To the right is a matrix showing network connections between query genes and each pathway. Each gene is shown as a coloured box and mouseover shows its number of links to the pathway. Green boxes represent query genes linked to the pathway and purple boxes indicate genes which are part of the pathway. Darker shades indicate higher connectivity.