PhyMycoProm Hard-Negative Promoter Benchmark

Dataset summary

PhyMycoProm is a cross-species benchmark for binary promoter recognition in three plant and two fungal species. It contains the 45,000-record hard-negative benchmark used in the manuscript: 22,500 experimentally supported promoters and 22,500 constructed negatives. Every sequence is 300 nt and contains only A, C, G and T.

The dataset provides DNA sequences, species annotations, binary labels, sample types, sequence quality metrics and leakage-control groups.

Species and sources

Each species contributes 9,000 records: 4,500 promoters, 2,250 shuffles, 1,125 gene-body negatives and 1,125 near-TSS negatives.

Code	Species	Kingdom	Promoter source	Reference genome and annotation
Ath	Arabidopsis thaliana	Plant	EPDnew 004	TAIR10; Ensembl Plants 62
Hvu	Hordeum vulgare	Plant	EPDnew 000	MorexV3; Ensembl Plants 62
Zma	Zea mays	Plant	EPDnew 001	B73 RefGen_v3; NCBI RefSeq GCF_000005005.1, Annotation Release 100
Sce	Saccharomyces cerevisiae	Fungus	EPDnew 002	R64-1-1; Ensembl Fungi 62
Spo	Schizosaccharomyces pombe	Fungus	EPDnew 002	ASM294v2; Ensembl Fungi 62

Fields and sample types

Field	Type	Meaning
sequence_id	string	Unique sample identifier; key for linking fold assignments and predictions
species	category	Ath, Hvu, Zma, Sce or Spo; see the species table above
sequence	string	Uppercase 300-nt DNA sequence
label	integer	1 for a promoter; 0 for a constructed negative
sample_type	category	promoter, shuffle, gene_body or near_tss; never empty
gc_content	float	Fraction of bases that are G or C, in [0, 1]
repeat_or_low_complexity_fraction	float	Fraction covered by the union of source repeat masking and the benchmark's short-DNA low-complexity mask, in [0, 1]
cv_group	string	Dependency-aware group that must remain intact when splitting data

sample_type	label	Count	Definition
promoter	1	22,500	EPDnew-supported window spanning [-249, +50] around the annotated TSS, oriented in the direction of transcription
shuffle	0	11,250	Non-identical shuffle of a promoter that preserves exact directed dinucleotide counts
gene_body	0	5,625	Window sampled from a coding sequence or intron
near_tss	0	5,625	Genomic window centred 500–2,000 bp upstream or downstream of an annotated TSS

The annotated TSS is at zero-based index 249 in positive sequences. The same index can be used as the model input anchor for negatives, but it is not an annotated TSS in those records.

Loading the data

After downloading phymycoprom.csv, load it with pandas:

import pandas as pd

df = pd.read_csv("phymycoprom.csv")
print(df.shape)  # (45000, 8)

Or with Hugging Face Datasets:

from datasets import load_dataset

dataset = load_dataset(
    "csv",
    data_files={"benchmark": "phymycoprom.csv"},
)["benchmark"]

Quality control

All positive promoters passed an exact comparison with the corresponding 60-nt EPDnew reference spanning [-49, +10]. Zma coordinate offsets were corrected only when a unique exact reference match was found within ±10 kb. Each negative was matched to a positive from the same species during construction; genomic negatives had an absolute GC-fraction difference of at most 0.02.

The filter repeat_or_low_complexity_fraction < 0.20 applies only to genomic negatives (gene_body and near_tss). Promoters and shuffled negatives can exceed this value. In this release, 4,931 promoters and 17 shuffles have values at least 0.20. All released sequences contain no ambiguous bases.

Validation also checks sample quotas, sequence length, dinucleotide preservation for shuffles and absence of group leakage in the recorded folds.

Intended uses and limitations

Use this benchmark for promoter classification, grouped model evaluation and cross-species or plant–fungal transfer analysis. It covers only five species and uses an artificial 1:1 class balance with constructed negatives; it does not estimate genome-wide promoter prevalence. Performance does not establish causal regulatory mechanisms or validate motif function.

Licence and redistribution status

The license: other metadata is intentional: no project-level open-data licence has been assigned. Before public release, verify the reuse and redistribution terms of the EPDnew, Ensembl and NCBI source material and select a compatible repository licence.

Citation

Repository: https://huggingface.co/datasets/YDXX/PhyMycoProm.

A dataset DOI has not yet been assigned. Cite the repository URL together with the accessed commit or revision.