Abstract: Provided are methods of modulating gene expression levels in an individual identified as having endometriosis. The methods comprise administering to the individual identified as having endometriosis a drug described herein in an amount effective to modulate gene expression levels in the individual. Also provided are pharmaceutical compositions. The compositions comprise a drug described herein in an amount effective to modulate gene expression levels in an individual, wherein the pharmaceutical composition is adapted for intrauterine or intravaginal administration of the drug to the individual. Kits that find use in practicing the methods of the present disclosure are also provided. In some embodiments, the kits comprise a pharmaceutical composition comprising a drug described herein in an amount effective to modulate gene expression levels in the individual, and instructions for administering the pharmaceutical composition to an individual identified as having endometriosis.