HOXD3 and neoplasm: This cluster was enriched in genes involved in differentiation and developmental processes (for example, SOX1 and SOX9, HOXD3 and HOXD8, and TBX4) and genes implicated as tumor suppressors (for example, SOX1 and SOX17, TSHZ3, WT1-AS, and FGF14) (Extended Data Fig. 1c and Supplementary Tables 1 and 2).