This focused collection explores inequalities in the experiences of women in physics. Yet, it is important for researchers to also be aware of and draw insights from common patterns in the experiences of women across science, technology, engineering and mathematics (STEM) disciplines. Here, we review studies on gender disparities across college STEM on measures that have been correlated with retention. These include disparities in academic performance, engagement, self-efficacy, belonging, and identity. We argue that observable factors such as persistence, performance, and engagement can inform researchers about what populations are disadvantaged in a STEM classroom or program, but we need to measure underlying mechanisms to understand how these inequalities arise. We present a framework that helps connect larger sociocultural factors, including stereotypes and gendered socialization, to student affect and observable behaviors in STEM contexts. We highlight four mechanisms that demonstrate how sociocultural factors could impact women in STEM classrooms and majors. We end with a set of recommendations for how we can more holistically evaluate the experiences of women in STEM to help mitigate the underlying inequities instead of applying a quick fix. [This paper is part of the Focused Collection on Gender in Physics.]