FANTOM4: Systems biology of a leukemia transcriptome and its regulation. This special collection of articles are the companion papers for the three FANTOM4 papers published withNature Genetics. FANTOM4 has used genome-wide expression profiling to measure the expression dynamics of promoter usage, mRNAs, microRNAs and other small non-coding RNAs throughout a time course of differentiation in the acute myeloid leukemia cell line THP-1. Of particular interest was the extensive use of deepCAGE (a new deep sequencing application) to identify active promoters and their expression dynamics. Computational analysis, chromatin immunoprecipitation and perturbation experiments have then been used to build network models of the transcription factors and miRNAs, their targets and their role in differentiation and maintenance of the undifferentiated state.