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license: cc-by-4.0
tags:
  - biology
  - gene-regulatory-network
  - foundation-model
  - cross-species-transfer
  - plant
  - Nicotiana-benthamiana

nbgrn-transfer — cross-species gene-regulatory-network transfer to Nicotiana benthamiana

Models, data, and inferred networks for the paper "Conditioning a gene-regulatory foundation model on transcription-factor sequence enables ortholog-free cross-species transfer: the Nicotiana benthamiana network from soybean and Arabidopsis."

A masked-expression gene-regulatory foundation model (GRN-FM) with a single explicit TF×target weight tensor W is trained in a data-rich source species (soybean or Arabidopsis) and transferred zero-shot to data-poor N. benthamiana — either through reciprocal-best-hit orthologs, or, with no ortholog lookup for the regulators, by a sequence-conditioned model whose TF rows are generated from ESM-2 protein embeddings (W = φ(ESM(TF))·Vᵀ). Transfer is scored by relatedness-aware leave-study-out prediction of tobacco's own held-out-study expression (no regulatory gold standard is used).

`models/`

file	description
`arabidopsis_grn_fm_W.npz`	Arabidopsis GRN-FM explicit weight tensor W (source)
`arabidopsis_grn_fm_seq_d256.pt`	Arabidopsis sequence-conditioned GRN-FM (φ + V, rank d=256; ESM-2 `esm2_t12_35M_UR50D`)
`soybean_grn_fm_W.npz`	Soybean GRN-FM weight tensor W (source; same model as the companion `dirmy/soygrn`)
`tobacco_within_grn_fm_W.npz`	Within-species tobacco GRN-FM W (upper-bound reference)

`data/`

file	description
`tobacco_gene_tpm.npz`	N. benthamiana compendium: 56,738 genes × 1,540 samples (NbT2T reference)
`tobacco_sample_meta.csv`	per-sample SRA Study/BioProject metadata (153 studies)
`tobacco_protein_esm2.npz`	ESM-2 mean-pooled embeddings of tobacco proteins
`tobacco_tf_genes.txt`	1,203 ortholog-defined candidate tobacco TFs
`tobacco_to_arabidopsis_rbh.tsv`	tobacco↔Arabidopsis reciprocal-best-hit orthologs (12,773)
`tobacco_to_soybean_rbh.tsv`	tobacco↔soybean reciprocal-best-hit orthologs (13,981)

`networks/`

Inferred TF→target edge lists (columns: TF, target, score): tobacco_within_clr.tsv, tobacco_within_grnboost2.tsv, tobacco_within_fm.tsv (within-species), and tobacco_transfer_from_arabidopsis.tsv (zero-shot Arabidopsis→tobacco transfer).

Reproduce

Code: https://github.com/k821209/nbgrn-transfer

python src/grn_transfer_eval.py     # ortholog transfer (soybean/Arabidopsis → tobacco)
python src/grn_transfer_seq.py      # sequence-conditioned, ortholog-free transfer
python src/grn_fewshot.py           # within-species data-efficiency curve

Companion

Within-species soybean GRN benchmark: dirmy/soygrn (DOI 10.57967/hf/9365).

Citation

Kang, Y. Conditioning a gene-regulatory foundation model on transcription-factor sequence enables ortholog-free cross-species transfer. (2026). Data & models: this repository.

License: CC-BY-4.0.

dirmy
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nbgrn-transfer