I believe you have IPA pathway guide with you. For IPA if you are doing pathway analysis with the differential analysis I believe and you did the core tox analysis. The most detailed way to do is to put both up and down regulated list of genes in the first column and then in the second column of the input file should be your log transformed fold-changes with sign. This will enable you to see for specific pathways which gene from your list are up/down regulated in the pathway of interest. One thing which I suggest is to use the species and the stringency filters before running the analysis. It should correspond to what species your data is from. Once you have the results you should be able to look into the tab of canonical pathways. You can customize for your target pathways as well or you can just filter for FDR and then select and download the pathway list. Then the tab delimited file you are using will show list of pathways with the enrichment and the p-value and the qvalue and you can sort the list according to your highest significance calls.