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ProRiboGen Datasets

Supporting data for ProRiboGen (protein-conditioned RNA generation): RBP–RNA training/test splits, motif logos / HOMER matrices, CLIP / generated evaluation sets, reviewed RBP catalogs, and cross-species resources.

Code: github.com/yuhuaJiao-tky/ProRiboGen
Model weights: yuhuajiaotky/ProRiboGen-weights

Dataset structure

train_test/
  337_RBPs_split/
  CLIP_Generated_test_logos/
  CLIP_test_fasta/
  CLIP_test_motif_matrix/
  Generated_test_fasta/
  Generated_test_motif_matrix/
ProRiboGen_CLIP_validation/
  A1CF/
    experimental/
    generated/
  NELFE/
    experimental/
    generated/
  YBX1/
    experimental/
    generated/
reviewed_RBPs/
  reviewed_11_species_RBPs/
  reviewed_1492_human_RBPs/
cross_species_RBPs/
  A.thaliana/ Chicken/ Fly/ Frog/ Macaque/ Mouse/
  Orangutan/ Rat/ Worm/ Yeast/ Zebrafish/
README.md

Path	Description
`train_test/337_RBPs_split/`	Train/test RBP–RNA tables (`ProRiboGen_train_RBP-RNA.csv`, `ProRiboGen_test_RBP-RNA.csv`) and `train_test_RBPs.xls`
`train_test/CLIP_*`	CLIP evaluation FASTA, motif matrices, and logos
`train_test/Generated_*`	Generated evaluation FASTA and motif matrices
`ProRiboGen_CLIP_validation/`	In-house CLIP validation for A1CF, NELFE, YBX1: each has `experimental/` (wet-lab sequences, motifs, logos) and `generated/` (ProRiboGen-generated sequences, motifs, logos) for paired comparison
`reviewed_RBPs/reviewed_1492_human_RBPs/`	Reviewed human RBPs: `motifs/`, `homer_motif_matrix/`
`reviewed_RBPs/reviewed_11_species_RBPs/`	Multi-species reviewed RBPs: `motifs/`, `homer_motif_matrix/`
`cross_species_RBPs/`	Per-species folders with `fasta/`, `motifs/`, `homer_motif_matrix/`

Train/test CSV columns (`train_test/337_RBPs_split/`)

p_id, protein, rna, r_id, s, t, score, type, p_len, r_len

Download

hf download yuhuajiaotky/ProRiboGen-datasets \
  --repo-type dataset \
  --local-dir ./ProRiboGen_dataset

Related resources

Resource	Link
Code	https://github.com/yuhuaJiao-tky/ProRiboGen
Weights	https://huggingface.co/datasets/yuhuajiaotky/ProRiboGen-weights

Citation

If you use this dataset, please cite the ProRiboGen paper / repository (update with the final citation when available).

@software{ProRiboGen,
  title  = {ProRiboGen: Protein-conditioned RNA generation},
  author = {Jiao, Yuhua and collaborators},
  url    = {https://github.com/yuhuaJiao-tky/ProRiboGen},
  year   = {2026}
}

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