The modENCODE Consortium clustered 10,733 genes into 34 groups based on the similarity of their expression profiles throughout development (FBrf0213979). This clustering analysis was based upon FlyBase gene annotations from October 2009 (release 5.22, FB2009_09). As of June 2012, 238 of the 10,733 FlyBase gene identifers provided by the authors had become obsolete and were replaced by newer gene identifiers; FlyBase identifier replacement indicates significant gene model changes that could potentially confound the RNA-Seq expression profile upon which the clustering analysis was based. The nature of these gene model changes was reviewed to determine whether or not it made sense to apply clustering assignments based on old gene models to the updated gene models. For 93 genes, clustering assignments were not appended to updated gene models because either the FlyBase 5.22 gene model was subsequently split into two independent genes, or because two FlyBase 5.22 gene models assigned to different clusters were later merged into a single gene. For 145 genes, cluster assignments were propagated to updated (merged) gene models because either the merged genes had the same cluster assignment or the merge involved an annotated gene and a previously unannotated gene (i.e., a gene with no gene model and inferred from genetic data only).