Additional file 4: of Comparison of discriminative motif optimization using matrix and DNA shape-based models

Table S4. AUPRC and AUROC differences between model pairs by TF. (XLSX 32 kb

Additional file 3: of Comparison of discriminative motif optimization using matrix and DNA shape-based models

Table S3. Scores for the motif optimization algorithms on ChIP-seq data with small training sets. (DOCX 12 kb

Additional file 1: of Comparison of discriminative motif optimization using matrix and DNA shape-based models

Table S1. Mean AUROC (and standard deviation) on ChIP-seq data. (DOCX 13 kb

Additional file 2: of Comparison of discriminative motif optimization using matrix and DNA shape-based models

Table S2. Effect of Method for Generating Negative Sequences on Training and Testing Scores. (DOCX 13 kb

MOESM2 of Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq

Additional file 2. Spec-seq results for BATFx-JUNB. Spec-seq results for BATF-JUNB (sheet1), BATF2-JUNB (sheet2), and BATF3-JUNB (sheet3). Each sheet contains a CRE part and TRE part. Only the single variants from the wild type target (TGACGTCA for CRE and TGAC/GTCA for TRE) were included in the tables. The number of counts in the bound and unbound bands are provided. The ration of bound/unbound are proportional to the relative binding affinities. Energy = −ln(ratio); energy units are kT (k = Boltzmann constant, T in degrees Kelvin)

MOESM7 of Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq

Additional file 7. Oligos used. Oligos used for PCR and sequencing