maize-genetics/plexbench-base

Dataset Card for Maize and Arabidopsis gene expression

Plant Gene expression data used for benchmarking sequence to gene expression prediction ML models.

Dataset Description

Species included are Maize and Arabidopsis thaliana. Dataset includes gene expression values for leaf and root tissues. Within the tasks folder, datasets are broken down by species-task-tissue. Genomes in the genomes folders include the annotation and the GFF files associated with that specific genome. All tasks are split by 80% train, 10% validation, and 10% test.

Dataset Structure

dataset
  genomes/
    Arabidopsis_thaliana/
      annotation.fa
      ath.gff
    Zea_mays/
      annotation.fa
      ath.gff
  tasks/
    species-task-tissue/
      train.tsv
      validate.tsv
      test.tsv

• Curated by: Taylor Ferebee, Travis Wrightsman, Jingjing Zhai, Aaron Gokaslan, Volodymyr Kuleshov, Edward S. Buckler
• Repository: [https://github.com/maize-genetics/expression-survey]
• Paper: PLExBench: A benchmarking suite for predicting gene expression in plants
• License: MIT

Dataset Sources

sample_name	species	genotype	library_layout	library_selection	reads_location	organ	age	condition	replicate	batch	reference
SRR505743	Arabidopsis_thaliana	Col-0	single-read	random	sra	root	seedling	controlled	1	1	SRP013631
SRR505744	Arabidopsis_thaliana	Col-0	single-read	random	sra	leaf	seedling	controlled	1	1	SRP013631
SRR953400	Arabidopsis_thaliana	Col-0	single-read	random	sra	leaf	seeding	controlled	1	1	PRJNA215448
SRR1005386	Arabidopsis_thaliana	Col-0	single-read	random	sra	leaf	seedling	controlled	1	1	PRJNA222364
SRR578947	Arabidopsis_thaliana	Col-0	single-read	random	sra	root	seedling	controlled	1	1	SRP013631
SRR578948	Arabidopsis_thaliana	Col-0	single-read	random	sra	root	seedling	controlled	1	1	SRP013631
ERR2096663	Zea_mays	B73	paired-end	polyA	sra	leaf	seedling	controlled	1	1	PRJEB22166
ERR2096664	Zea_mays	B73	paired-end	polyA	sra	leaf	seedling	controlled	1	1	PRJEB22166
ERR2096665	Zea_mays	B73	paired-end	polyA	sra	leaf	seedling	controlled	1	1	PRJEB22166
ERR2096666	Zea_mays	B73	paired-end	polyA	sra	leaf	seedling	controlled	1	1	PRJEB22166
ERR2096667	Zea_mays	B73	paired-end	polyA	sra	leaf	seedling	controlled	1	1	PRJEB22166
ERR3773807	Zea_mays	B73	paired-end	polyA	sra	root	seedling	controlled	1	1	PRJEB35943
ERR3773808	Zea_mays	B73	paired-end	polyA	sra	root	seedling	controlled	1	1	PRJEB35943
ERR986091	Zea_mays	B73	paired-end	random	sra	root	seedling	controlled	1	1	PRJEB10406

Curation Rationale

To choose experiments for leaf and root tissues, we focused on datasets that have been used in a recent study and can be found in multiple databases.

Data Collection and Processing

In the max gene expression datasets, for each gene, we take the maximum transcript per million TPM value over experiments. Similarly, for the absolute expression datasets, we take the mean TPM value over experiments. Finally, for the on-off ex- pression, we assign 1 to a gene if it has a TPM value in one of the tissues. To create train-test-validation splits, we use orthogroup guided splitting as introduced by Washburn et al. 2019. Then, we split the training test sets so that we train on 80% of the orthogroups and test on 10%. Note that for each of the task-based datasets, we keep the same train-test-validate split.

BibTeX:

Dataset Card Authors

Taylor Ferebee (tf259@cornell.edu)

Dataset Card Contact

Taylor Ferebee (tf259@cornell.edu), Cinta Romay, Edward S. Buckler