Supplementary Table S3 from Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes

Differential regulation metrics and values for select features
Sheet 1: Log2 fold-change, p-value, and q-value between ARPC and NEPC lines for NPS in the 47 phenotype defining gene bodies (two tailed Mann-Whitney U test, Benjamini-Hochberg adjusted).
Sheet 2: Differentially expressed list of 514 transcription factor (TF). All statistical comparison and fold change estimation was done against ARPCs.
Sheet 3: Log2 fold-change, p-value, and q-value between ARPC and NEPC lines for central mean coverage in 108 TFs overlapping RNA-Seq up/down regulated TFs (two tailed Mann-Whitney U test, Benjamini-Hochberg adjusted).
Sheet 4: Paralogous transcription factors (TFs) for each of the 38 TFs with differential RNA expression between ARPC and NEPC and differential TFBS accessibility. Paralogous TFs that are also differentially expressed by RNAseq analysis of PDX tumors are shown in red text. Paralogs were obtained from ensembl biomart human genes GRCh38.p13 (http://uswest.ensembl.org/biomart/martview/64d8bd7fe9851a2501aece9b74b03631)
Sheet 5: Mean values in ARPC, NEPC, and HD lines for central and window means for ARPC and NEPC specific open chromatin regions.