Fig. 4. Evaluation of the overlap between the predicted complex and the standard Retromer complex.

The Retromer complex, as annotated by IntAct, serves as a benchmark to assess the performance of various methods in module identification. This standard complex consists of five members: PEP8, VPS35, VPS29, VPS17, and VPS5. The degree of overlap between the predicted complexes and the standard complex is measured using the Jaccard index. Purple indicates that the predicted member is part of the standard complex, gray indicates that the predicted member is not part of the standard complex, and green denotes that a member from the standard complex has not been captured by the prediction.