Table 1.
Small- and large-scale experimental methods to explore transcription factor–target gene interactions or transcription factor binding sites
| Evidence type | Method name | Reference |
|---|---|---|
| Small-scale | DNase-I footprinting | Galas DJ & Schmitz, 1978 (2) |
| EMSA: electrophoretic mobility shift assay | Garner MM & Revzin A, 1981 (3) | |
| SELEX: systematic evolution of ligands by exponential enrichment | Pollock R & Treisman R, 1990 (4) | |
| Promoter deletion analyses coupled to reporter assays | de Wet JR, et al., 1987 (5) | |
| Large-scale: in vitro | ChIP-on-chip: chromatin immunoprecipitation with DNA microarray | Ren B, et al., 2000 (6) |
| HT-SELEX: high-throughput systematic evolution of ligands by exponential enrichment | Jolma A, et al., 2010 (7) | |
| MITOMI: Mechanically induced trapping of molecular interactions | Rockel S, et al., 2012 (8) | |
| Large-scale: in vivo | ChIP-seq: chromatin immunoprecipitation coupled with high-throughput sequencing | Johnson DS, et al., 2007 (9); Robertson G, et al., 2007 (10) |