Protocol to predict the origin of cancer of unknown primary from gene expression data using BPformer

Patients diagnosed with cancer of unknown primary (CUP) have poor prognoses, highlighting the need to identify primary sites for targeted therapeutic intervention. Here, we present a protocol to predict the primary sites of CUP based on gene expression data using BPformer. We describe steps for installing software, collecting and preprocessing data, and training the BPformer model. We then detail procedures on using BPformer via a visualized web server. For complete details on the use and execution of this protocol, please refer to Xie et al.¹.