Additional file 2 of Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma

Additional file 2: Table S1. Results from Allele-Specific Expression (ASE) analysis of RNA-seq data for 96 neuroblastoma samples from TARGET. Table S2. Number of significant (FDR ≤ 0.1 or 10%) and testable (i.e., at least 1 heterozygous site with ≥ 10 reads) samples for neuroblastoma tumors, adrenal gland, and whole-blood tissues for all significant ASE genes. Genes were considered to have neuroblastoma-specific ASE if they met these criteria; a) testable in ≥ 10 neuroblastoma and normal (i.e., adrenal-gland and whole-blood) samples and b) significant in ≥3 neuroblastoma and significant ≤ 1 normal sample. The prefix “r.” indicates the number of samples showing significant ASE and “N.” indicates the number of samples testable for ASE. Table S3. Top 20 Gene Ontology (Biological processes) categories enriched for 1,043 NB-ASE genes. Table S4. SCNA scores for 96 neuroblastoma patient samples. Table S5. Spearman’s correlation between ASE (aRNA) for 1,043 NB-ASE genes and SCNA score for overlapping genomic segments. Table S6. Table of high-impact somatic mutations mapping to NB-ASE genes detected using exome-seq data using Variant Effect Predictor (VEP) in 96 neuroblastoma tumors. Table S7. Spearman’s correlation between ASE (aRNA) and mean promoter methylation for 1,043 NB-ASE genes. Table S8. Spearman’s correlation between ASE (aRNA) and gene expression (z-score normalized Fragments per Kilobase Per Million mapped) for 1,043 NB-ASE genes.