The present invention provides methods for measuring the total and/or activation levels of one or more analytes such as HER1, HER2, HER3, cMET, IGF-1R, PI3K, AKT, PRAS40, MEK, RSK, JAK1, STAT1, STAT3, TNFα, and/or anti-TNFα drug to determine whether a subject with inflammatory bowel disease (IBD) has non-inflamed and/or non-involved or inflamed and/or involved gastrointestinal tissue. The methods of the present invention can be used to evaluate mucosal healing, to diagnose, prognose, and monitor the progression of IBD, and to select and monitor the therapeutic response to IBD therapy.