Many firms these days are opting to specialize rather than generalize as a way of maintaining their competitiveness. Consequently, they cannot rely solely on themselves, but must cooperate by combining their advantages. To obtain the actual condition for this cooperation, a multi-layered network based on two different types of data was investigated. The first type was transaction data from Japanese firms. The network created from the data included 961,363 firms and 7,808,760 links. The second type of data were from joint-patent applications in Japan. The joint-patent application network included 54,197 nodes and 154,205 links. These two networks were merged into one network. The first anaysis was based on input-output tables and three different tables were compared. The correlation coefficients between tables revealed that transactions were more strongly tied to joint-patent applications than the total amount of money. The total amount of money and transactions have few relationships and these are probably connected to joint-patent applications in different mechanisms. The second analysis was conducted based on the p* model. Choice, multiplicity, reciprocity, multi-reciprocity and transitivity configurations were evaluated. Multiplicity and reciprocity configurations were significant in all the analyzed industries. The results for multiplicity meant that transactions and joint-patent application links were closely related. Multi-reciprocity and transitivity configurations were significant in some of the analyzed industries. It was difficult to find any common characteristics in the industries. Bayesian networks were used in the third analysis. The learned structure revealed that if a transaction link between two firms is known, the categories of firms' industries do not affect to the existence of a patent link.