Roadmap Enhancer-Gene Links

Prediction of enhancer-gene links for each Roadmap Epigenomics reference epigenome is available in a 212MB zip file. 

Download zip file

Files in the zipfile have the naming links_EPIGENOMEID_ENHANCERSTATE_2.5.txt.

EPIGENOMEID corresponds to the ID of the Reference Epigenome. 

Meta-data for the reference epigenome

ENHANCERSTATENUMOF15STATEOBSERVEDMODEL corresponds to the state number of one of the candidate enhancer chromatin states from the 15-state observed model from (Roadmap Epigenomics Consortium et al, 2015). Predictions have been made separately for states 6_EnhG, 7_Enh, and 12_EnhBiv and for each reference epigenome.
 

The files are six-column tab delimited with the columns as follows:

  1. chromosome
  2. start coordinate of 200-bp bin (0-based inclusive; hg19)
  3. end coordinate of 200-bp bin (0-based exclusive; hg19)
  4. ensembl gene ID
  5. prediction confidence score
  6. position relative to TSS

Predictions are made separately for each 200bp bin. Only enhancer-gene links with a confidence score greater than or equal to 2.5 are included in the file.
The general approach to generate these links was described in (Ernst et al, 2011) with specific changes described in (Liu et al, 2017).
The data used to generate these links was described in (Roadmap Epigenomics Consortium et al, 2015).

Access code used to generate the links, which also uses the Weka software.

References

  • Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE.
    Mapping and analysis of chromatin state dynamics in nine human cell types.
    Nature 473: 43-49, 2011.
  • Liu Y, Sarkar A, Kheradpour P, Ernst J, Kellis M.
    Evidence of a recombination rate valley in human regulatory domains.
    Genome Biology 18: 193, 2017.
  • Roadmap Epigenomics Consortium, Kundaje A*, Meuleman W*, Ernst J*, Bilenky M*, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.
    Integrative analysis of 111 reference human epigenomes.
    Nature, 518:317-330, 2015.
    Supporting Website