High-resolution computational models of genome binding events

Yuan Qi, Alex Rolfe, Kenzie D MacIsaac, Georg K Gerber, Dmitry Pokholok, Julia Zeitlinger, Timothy Danford, Robin D Dowell, Ernest Fraenkel, Tommi S Jaakkola, Richard A Young & David K Gifford

Supplementary Fig. 1 (pdf 55K)
CHIP-chip experimental protocol.

Supplementary Fig. 2 (pdf 110K)
Enrichment ratios for three replicates of an untagged control experiment and two replicates of Mig2.

Supplementary Fig. 3 (pdf 120K)
Motif discovery output.

Supplementary Fig. 4 (pdf 50K)
Influence function for yeast, human embryonic stem cells and human liver.

Supplementary Table 1 (pdf 20K)
MIPS categories of Gen4 targets identified by JBD.

Supplementary Table 2 (pdf 25K)
Known Gen4 and Mig2 log-odds weight matrix as discovered by motif discovery with positional priors from JBD and as previously published by Haribson et al. and Luftiya et al.

Supplementary Table 3 (pdf 35K)
Performance (median distance in bp) of JBD on synthetic data.

Supplementary Table 4 (pdf 35K)
Standard error of the mean spatial resolution of JBD on synthetic data.

Supplementary Table 5 (pdf 20K)
Mean distance in nucleotides between binding calls and Gen4 motif in 573 promoter regions with a conserved Gen4 motif.

Supplementary Discussion (pdf 10K)

Supplementary Methods (pdf 75K)

Supplementary Data 1 (txt 1K)

Supplementary Data 2 (txt 10K)

Supplementary Data 3 (txt 5K)

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