HLA PTM Analysis (HLA-I + HLA-II)

Analysis of post-translational modifications on HLA class I and class II presented peptides from the JY cell line, for the PTM-stability manuscript.

Caron Laboratory, Yale University

Repository layout

Where	What
repo root	HLA-I pipeline (data_loader.R, Figure*.R) and its outputs in figure_panels/
HLA-II/	HLA-II pipeline (scripts/) and its outputs in HLA-II/figure_panels/
shared/	Canonical PTM order + color palette (ptm_config.R) and the shared circos renderer (circos_draw.R), sourced by both pipelines

The two pipelines produce side-by-side manuscript panel pairs: each pair uses the same PTM order, the same per-PTM colors, the same legend sizes and the same export dimensions (shared/ptm_config.R::PAIR_DIMS). Manuscript panels carry no titles; PNG (300 dpi), PDF and TIF (300 dpi LZW) are written for every pair panel.

Data

• Cell line: JY (HLA-I: A*02:01, B*07:02, C*07:02; HLA-II: DPA1/DPB1, DQA1/DQB1, DRA1/DRB1 alleles)
• Peptide lengths: HLA-I 8-14, HLA-II 10-25
• 13 biological PTMs per class (incl. Nitrosylation) + artifact oxidation
• Source files (not tracked; obtain from M. Shahbazy):
  • HLA-I_JY_DDA_PTMs_ResultsSummary_01262026_3.xlsx (repo root)
  • HLA-II_JY_DDA_PTMs_ResultsSummary_05012026_4.xlsx (in HLA-II/)
• HLA-II sheets carry the NetMHCIIpan 9-mer binding Core per peptide; the loader exports Core/CoreStart/CoreSite, which drive the core-based P1-P9 positional figures (Figure4C2, Figure4X3/4X4).

Usage

# HLA-I (from repo root)
Rscript run_all_figures.R

# HLA-II
cd HLA-II && Rscript run_all_figures_hla2.R

Intermediate data CSVs in each figure_panels/ are regenerated by the loaders and tracked for reproducibility. HLA-II/figure_panels/validation_counts.csv cross-checks every canonical PTM count against the embedded per-sheet summaries of the source workbook.