Research on fostering learning about percentages within intelligent tutoring systems (ITSs) is limited. Additionally, there is a lack of data-driven approaches for improving the design of ITS to facilitate learning about percentages. To address these gaps, we first investigated whether students' understanding of basic mathematical skills (eg, arithmetic, measurement units and geometry) and fractions within an ITS predicts their understanding of percentages. We then applied a psychological network analysis to evaluate interdependencies within the data on 44 subtopics of basic mathematical concepts, fractions and percentages. We leveraged a large-scale dataset consisting of 2798 students using the ITS "bettermarks" and working on approximately 4.1 million mathematical problems. We found that advanced arithmetic, measurement units, geometry and fraction understanding significantly predicted percentage understanding. Closer inspection indicated that percentage understanding was best predicted by problems sharing similar features, such as fraction word problems and fraction/natural number multiplication/division problems. Our findings suggest that practitioners and software developers may consider revising specific subtopics which share features with percentage problems for students struggling with percentages. More broadly, our study demonstrates how evaluating interdependencies between subtopics covered within an ITS as a data-driven approach can provide practical insights for improving the design of ITSs.