From microarray platform I have selected 35 genes involved in two different metabolic pathway, Can I use these genes or probesets to generate GESA (gene set enrichment analysis plot) from Broad institute?
Yes you can. You only need to generate a new gene-set (gmt file) including your 35 gene-list of interest and then run the GSEA using this new gene-set. So first generate the gmt file with your signature and load it in GSEA and next run the GSEA using the entire gene expression matrix (after preprocessing filtering) as input (gct file).