In the end, we identified 11 putative biomarkers, including HMGCS2, CHL1, DAO, CRTAC1, EDN1, WNT10A, HBEGF, IL6, CCK, EPHA3 and SEMA3E, in the core IPF gene set (details in Additional file 10: Table S4) which is the smallest biomarker set that allowed >0.8 specificity and 0.9 sensitivity in distinguishing IPF from healthy control. Here, EPHA3 is linked to idiopathic pulmonary fibrosis.