Background: The pulmonary arteries are the blood vessels that carry blood from the right side of the heart through the lungs. Pulmonary arterial hypertension (PAH) is a progressive disorder characterized by higher pressure of lungs pulmonary artery for no apparent reason. PAH is treatable although there is no clear cure for the disease. Fortunately, human genomics have been decoded in 2004 and several molecular targeting compounds related to PAH were discovered, the uncured disease should give clinical scientists and medical doctors new scenery to develop some new modules to administer patients. Methods: We used a set of genomic data from clinical PAH to combine traditional medication and molecular target therapy so that integration modules will be used to the clinical field. The integration model had primarily relied on system biology including network, topology and gene-drug interaction database. Results: In this research article, we firstly analyzed using genomic expression signature from a set of clinical PAH genomic data and three known PAH pathways and then we combined current medications and molecular targeting therapy into the integration model. Conclusion: In the near future, we will develop a second-generation model based on the module by using individual clinical genomic data from different patients such as patient genomic data, clinical information including patient symptom and laboratory results.