Gene ontology (GO) is a repository that is used to define the gene with predefined set of diseases in a genomic set of data. The repository contains list of gene with unique id to identify the disease. Each process in gene is referred to as annotation. The analysis used in the gene is Association Rules (AR) which discovers biologically data. In existing work we used gene ontology weighted association rule which is used to find the frequent sets of gene with weighted sets. We are proposing mine cross ontology to find the Protein from the average sets of protein identified from the dataset. Our proposed system focus on cross ontology to find the disease based on the values obtained and the regulatory modules contains miRna, transcription factor and gene are used to ident ify the disease based on particular gene. Depth first search is used in our proposed system to identify the symptoms and precautions at depth level. Finally Bayesian rose tree analysis will produce the result in hierarchical structure.