I think this would be better as two sentences. The two verbs separated by "and" are not parallel.
"Therefore, the aim of our study was to evaluate the mutational frequency and expression pattern of two proinflammatory cytokine genes (IL-1b and IL-6) in the pulmonary tissues of immunocompromised mice (infected with A. fumigatus or A. flavus). We then compared the data with that of the respective immunocompetent mice in order to elucidate the role of the cytokines within the pulmonary tissues in propagation of the infection at the molecular level."
Note the change in spelling of "fumigatus". I changed "their role" because, as it was written, "their" referred to immunocompetent mice. I do not understand the use of the word "respective". Unless it is needed, I would delete "the respective".
Student or Learner