supp

Supplementary Material for:

ab initio prediction of transcription factor targets
using structural knowledge

Tommy Kaplan^1,2 Nir Friedman¹ and Hanah Margalit^2,*

¹ School of Computer Science & Engineering, The Hebrew University, Jerusalem 91904, Israel.

² Dept. of Molecular Genetics and Biotechnology, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel.

^* Corresponding author. Email: hanah@md.huji.ac.il

Dataset of canonical Cys₂His₂ zinc finger proteins and their target binding sites
Based on TRANSFAC 7.3.

Classification of zinc finger domains in TRANSFAC 7.3 to canonical (EGR-like) and non-canonical fingers

The classification was done using a Profile HMM of known canonical Cys₂His₂ zinc fingers, using HMMER 2.0

Predicted Binding Sites in Putative Target genes of 29 canonical Cys₂His₂ zinc finger proteins in D. melanogaster

Genome-wide predictions were performed using the predicted binding site models, on 2Kb upstream regions from FlyBase (See methods). For each gene, we present all significant putative binding sites (Bonferroni corrected p-value ≤ 0.05).