HT-SELEX

HT-SELEX (High-Throughput Systematic Evolution of Ligands by EXponential enrichment) is an in vitro experimental protocol that involves an iterative procedure that starts with an initial library of random oligonucleotides (oligos) of fixed length of either 20 or 40bp. Since this binding happens outside a cellular environment, it represents a TF’s intrinsic DNA-binding preferences. At every iteration of the procedure, the input pool of oligos compete to bind to the TF. Oligos that do not bind at all or bind weakly are washed out from the pool while the rest are amplified using PCR. A sample of the amplified pool is sequenced to allow for computational analysis while the rest of the pool is used as input for the subsequent selection round. In this way, at the end of each round there are more high-affinity oligos in the pool than before, while non-binders and weaker binders are gradually eliminated.

We used the filtered HT-SELEX probes from Yuan et al. [7] for training our models. Briefly, this dataset contains HT-SELEX data sequenced in Jolma et al. [18] (ENA accession ERP001824) and in Yang et al. [39] (ENA accession ERP016411), which together constitute 547 experiments for 461 human or mouse TFs. The experiments that were filtered out were those showing: 1) poor consistency of 8-mer enrichment in consecutive HT-SELEX cycles, 2) low number of enriched probes, or 3) low diversity of probe enrichment. For each remaining experiment, the top 2,000 enriched 20-bp probes were selected per experiment. The filtered dataset contains 325 high quality experiments covering 296 TFs.