A full listing of the Supplementary Figures and Tables is provided in the Supplementary file “ENCODE Supplementary Figures and Tables.docx”. Additional tables are provided as stand alone files as detailed in the index of “ENCODE Supplementary Figures and Tables.docx”. The file “ENCODE Supplementary Info.docx” contains detailed analysis methods and descriptions of code provided, along with descriptions of additional analysis and figures. The supplementary information is accompanied by a Virtual Machine (VM) containing the functioning analysis data and code. Further details of the VM are available from http://encodeproject.org/ENCODE/integrativeAnalysis/VM
