Supplementary Information for: Identification of genes associated with chemotherapy cross-resistance and treatment response in childhood acute lymphoblastic leukemia. Sanne Lugthart 1,2,6,8 , Meyling H. Cheok 1,2,8 , Monique L. den Boer 6 , Wenjian Yang 1,2,5 , Amy Holleman 6 , Cheng Cheng 3 , Ching-Hon Pui 1,4,5 , Mary V. Relling 1,2,5 , Gritta E. Janka-Schaub 7 , Rob Pieters 6,9 , William E. Evans 1,2,5,9 1 Hematological Malignancy Program 2 Department of Pharmaceutical Sciences 3 Department of Biostatistics 4 Department of Hematology-Oncology ,St. Jude Children's Research Hospital , Memphis , USA 5 The Pharmacogenetics of Anticancer Agents Research Group in the Pharmacogenetics Research Network, Memphis , Tennessee , USA 6 Department of Pediatric Oncology/Hematology ,Erasmus University Medical Center/Sophia Children's Hospital, ,Rotterdam , The Netherlands 7 COALL study group ,Children's University Hospital , Hamburg , Germany 8 These first authors contributed equally to this work. 9 These last authors contributed equally to this work.

Supplemental Table 6: Transcription factor binding sites over-represented in the sub-cluster of genes over-expressed in VCR-ASP discordant resistant ALL.

The promoter region and the 5'UTR for specific sets of genes was used for MatchT to search the most recent TRANSFAC^® Professional 8.1 database (vertebrates) (http://www.biobase.de/) for common regulatory elements. We determined statistical over-representation of the common motifs compared to "all" (~20,000) human promoter sequences (UCSC hg17; CLOVER) (Matys et al., 2003) and additionally we used the promoter sequences of the "other" gene set as background.
We found a total of 152 common transcription factor binding sites in the promoter regions of these 59 genes (3kb 5' of the transcription start site). Furthermore, we found significant over-representation of the same set of common transcription factor binding sites when sequences were compared against either "all" human promoter sequences or against the "other" 200 protein synthesis related genes. All these transcription factors are expressed in ALL cells except HEN1, but only ELF-1 was expressed at a significantly different level in ALL cells that were VCR-sensitive plus ASP-resistant versus VCR-resistance plus ASP-sensitive (P=0.014, t-test, R/S ratio =1.28).