Identifying gene expression modules that define human cell fates

•Development of an algorithm, CEMA, for identification of cell specific expression modules•Ectopic expression of CEMA selected transcription factors can derive partial reprogramming of fibroblasts.•hPSC engineered to express CEMA factors displays robust differentiation capacity towards a mature progeny.

Using a compendium of cell-state-specific gene expression data, we identified genes that uniquely define cell states, including those thought to represent various developmental stages. Our analysis sheds light on human cell fate through the identification of core genes that are altered over several developmental milestones, and across regional specification. Here we present cell-type specific gene expression data for 17 distinct cell states and demonstrate that these modules of genes can in fact define cell fate. Lastly, we introduce a web-based database to disseminate the results.