The present invention relates to biomarker genes for diagnosing and treating diseases. Provided herein are systems and methods of diagnosing a disease in a patient based on the patient's expression levels of biomarker genes. Examples of the TL1A-associated disease include, but are not limited to, an inflammatory bowel disease (IBD), Crohn's disease (CD), ulcerative colitis (UC), and fibrosis. Also provided herein are systems and methods of identifying a patient likely to be responsive to an anti-TL1A therapy, prescribing and/or administrating an anti-TL1A therapy to the patient based on the patient's expression levels of biomarker genes.
