Data for Intersection of Regulatory Analysis and Signature Reversion Uncovers Therapeutic Drugs and Targets for SETBP1-HD

This repository contains the processed data, pipeline outputs, and compiled results accompanying the manuscript Intersection of Regulatory Analysis and Signature Reversion Uncovers Therapeutic Drugs and Targets for SETBP1-HD. The data encompasses the full analytical pipeline, from processed RNA-seq read counts to differentially expressed genes (DEGs), consensus signatures, spatiotemporal permutation results, and drug repurposing candidates for SETBP1 Haploinsufficiency Disorder (SETBP1-HD). setbp1_hd/data Curated Targets: 260403_setbp1_targets.csv: A comprehensive, manually and computationally curated list of established and predicted SETBP1 regulatory targets compiled from 15 databases and literature review. DailyMed Data: drug_safety_data.tar.gz: Black box warnings, pediatric indications, pregnany risks, and blood-brain-barrier parsed sections from drug candidate labels, accessed via DailyMed API 260410. Processed RNA-seq Data: cardo.tar.gz, shaw.tar.gz, tanaka.tar.gz: Complete nf-core/rnaseq pipeline outputs (including FastQC, MultiQC, Salmon quantification, and STAR alignments) for the respective public datasets. cleaned_counts_data.tar.gz: Cleaned and formatted RNA-seq count matrices for downstream analysis from Cardo, Shaw, and Tanaka. wong.tar.gz: Curated supplementary data from Wong et al. (2025) utilized for downstream signature validation. setbp1_hd/results Results (results_*.tar.gz): results_eda.tar.gz: Exploratory data analysis (EDA) results, including PCA, combined dataset metadata, and random forest feature importance plots. results_dea.tar.gz: Differential expression analysis (DEA) outputs across all individual models and contrasts across datasets. results_consensus_signature.tar.gz: Results from consensus signature derivation, including Robust Rank Aggregation (RRA) and effect-size meta-analysis scoring. results_signature_reversion.tar.gz: Outputs from LINCS L1000 queries, including weighted connectivity scores (WTCS) and prioritized drug targets and candidates. results_permutation_analysis.tar.gz: Spatiotemporal permutation testing statistics and developmental window expression data generated using BrainSpan and GTEx databases. results_figures.tar.gz: Final compiled publication figures. setbp1_hd/checksums md5 checksums for individual files from data/ and results/