| ## Dataset Overview | |
| This dataset features the 7 evaluation tasks presented in the AgroNT (A Foundational Large Language Model for Edible Plant | |
| Genomes) paper. The tasks cover single output regression, multi output regression, binary classification, and multi-label classification which | |
| aim to provide a comprehensive plant genomics benchmark. Additionally, we provide results from in silico saturation mutagenesis analysis of sequences | |
| from the cassava genome, assessing the impact of >10 million mutations on gene expression levels and enhancer elements. See the ISM section | |
| below for details regarding the data from this analysis. | |
| | Task Name | # of Datasets(Species) | Task Type | Sequence Length (base pair) | | |
| | -------- | ------- | -------- | ------- | | |
| | Polyadenylation | 6 | Binary Classification | 400 | | |
| | Splice Site | 2 | Binary Classification | 398 | | |
| | LncRNA | 6 | Binary Classification | 101-6000 | | |
| | Promoter Strength | 2 | Single Variable Regression | 170 | | |
| | Chromatin Accessibility | 7 | Multi-label Classification | 1000 | | |
| | Gene Expression | 6 | Multi-Variable Regression | 6000 | | |
| | Ehancer Region | 1 | Binary Classification | 1000 | | |
| ## Dataset Sizes | |
| | Config Name | # Train Samples | # Validation Samples | # Test Samples | | |
| | -------- | ------- | -------- | ------- | | |
| |poly_a.arabidopsis_thaliana|170835|---|30384| | |
| |poly_a.oryza_sativa_indica_group|98139|---|16776| | |
| |poly_a.trifolium_pratense|111138|---|13746| | |
| |poly_a.medicago_truncatula|47277|---|8850| | |
| |poly_a.chlamydomonas_reinhardtii|90378|---|10542| | |
| |poly_a.oryza_sativa_japonica_group|120621|---|20232| | |
| |splicing.arabidopsis_thaliana_donor|2588034|---|377873| | |
| |splicing.arabidopsis_thaliana_acceptor|1704844|---|250084| | |
| |lncrna.m_esculenta|4934|---|360| | |
| |lncrna.z_mays|8423|---|1629| | |
| |lncrna.g_max|11430|---|490| | |
| |lncrna.s_lycopersicum|7274|---|1072| | |
| |lncrna.t_aestivum|11252|---|1810| | |
| |lncrna.s_bicolor|8654|---|734| | |
| |promoter_strength.leaf|58179|6825|7154| | |
| |promoter_strength.protoplast|61051|7162|7595| | |
| |gene_exp.glycine_max|47136|4803|4803| | |
| |gene_exp.oryza_sativa|31244|3702|3702| | |
| |gene_exp.solanum_lycopersicum|27321|3827|3827| | |
| |gene_exp.zea_mays|34493|4483|4483| | |
| |gene_exp.arabidopsis_thaliana|25731|3401|3402| | |
| |pro_seq.m_esculenta|16852|1229|812| | |
| ## In Silico Saturation Mutagensis | |
| ### File structure for: Mesculenta_305_v6_PROseq_ISM_LOG2FC.txt.gz | |
| Intergenic enhancer regions based on Lozano et al. 2021 (https://pubmed.ncbi.nlm.nih.gov/34499719/) <br> | |
| Genome version: Manihot esculenta reference genome v6.1 from Phytozome <br> | |
| CHR: Chromosome <br> | |
| POS: Physical position (bp) <br> | |
| REF: Reference allele <br> | |
| ALT: Alternative allele <br> | |
| LOG2FC: Log fold change in Intergenic enhancer probability (log2(p_mutated_sequence / p_original_sequence)) <br> | |
| ### File structure for: Mesculenta_v6_GeneExpression_ISM_LOG2FC.txt.gz | |
| Gene expression prediction based on: Wilson et al. 2016 (https://pubmed.ncbi.nlm.nih.gov/28116755/) <br> | |
| Genome version: Manihot esculenta reference genome v6 from Ensembl 56 <br> | |
| CHR: Chromosome <br> | |
| POS: Physical position (bp) <br> | |
| REF: Reference allele <br> | |
| ALT: Alternative allele <br> | |
| GENE: Gene ID <br> | |
| STRAND: Gene strand <br> | |
| TISSUE: Tissue type (Acronyms detailed in Figure 1 of Wilson et al.) <br> | |
| LOG2FC: Gene expression log fold change (log2(gene_exp_mutated_sequence / gene_exp_original_sequence)) <br> |