| | --- |
| | license: mit |
| | pretty_name: BrentLab Yeast Genome Resources |
| | language: |
| | - en |
| | --- |
| | # BrentLab Yeast Genome Resources |
| |
|
| | This Dataset stores resources meant to aid in the exploration of yeast -omic data, |
| | curated by the Brent Lab. |
| |
|
| | ## Terminology |
| |
|
| | Across all datasets in the BrentLab collection, we use the following terms consistently |
| |
|
| | - **locus_tag**: The systematic ID of an ORF. Eg, YKL038W |
| | - **symbol**: The common name of an ORF. Eg, RGT1 |
| | - **target**: when the genomic locus is the 'target' of location of measurement, then |
| | it is referred to as a 'target'. Eg, in RNAseq, the column `target_locus_tag` would |
| | store the counts over that gene. |
| | - **regulator**: This collection is made up of binding location assays, and perturbation |
| | of transcription factors and chromatin interacting proteins, which I refer to generally |
| | as 'regulators' |
| | |
| | This repo provides the following: |
| | |
| | You can find these by clicking on the [files and versions](https://huggingface.co/datasets/BrentLab/yeast_genome_resources/tree/main) tab. The file format is noted. |
| | |
| | - **brentlab_features** (csv): This is a simplified version of the |
| | SGD S288C-R64-3-1 annotations. We have used this file to standardize target |
| | and regulator `locus_tag` and `symbol` across the other datasets in this collection. |
| | - **yiming_promoters** (bed): The promoter regions used in |
| | [Kang et al in the Dual threshold optimization paper](https://genome.cshlp.org/content/30/3/459). |
| | These promoter regions are used for callingcards. |
| | - **mindel_promoters** (csv): The promoters used by the Barkai lab to evaluate the |
| | overlap between perturbation and binding in the Mahendrawada 2025 set in |
| | [this preprint](https://www.biorxiv.org/content/10.1101/2025.10.12.681120v1.abstract). |
| | See scripts/create_promoter_bed_from_mindel.R. The column `in_mahendrawada_features` is |
| | `TRUE` if the locus_tag is in the feature set used by Mahendrawada 2025, which is |
| | only protein coding genes which are not labeled dubious. The column `promoter_exact_aligns` |
| | provides a tally of how many times the promoter sequence aligns exactly from end to end |
| | with no gaps in the genome. Most align only once, which is what we would expect for a |
| | 700+ bp sequence. However, there are 12 loci with up to 4 exact alignments. I didn't examine |
| | these beyond confirming the multiple alignments -- I suspect that it is due to repeat regions. |
| | It is noted because it is surprising that such long sequences had multiple perfect alignments. |
| | - **gal_tss_sgd-5-1_verified_orf** (bed): Genomic coordinates of Transcription Start Sites |
| | (TSS) for verified ORFs under Galactose culture conditions. These are derived from |
| | annotation version S288C-R64-5-1. See scripts/create_tss_files.R |
| | - **median_across_conds_tss_sgd-5-1_verified_orf** (bed): Median Transcription Start Site |
| | (TSS) coordinates for verified ORFs aggregated across different experimental |
| | conditions. See scripts/create_tss_files.R |
| | - **ypd_tss_sgd-5-1_verified_orf** (bed): Genomic coordinates of Transcription Start Sites |
| | (TSS) for verified ORFs under standard YPD (rich medium) culture conditions. |
| | See scripts/create_tss_files.R |
| | - **intergenic_regions_5_1** (bed and fasta): Both the genomic coordinates and sequences |
| | of the intergenic regions in version S288C-R64-5-1. See scripts/parse_intergenic_regions.R |
| | - **chrmap** (csv): This file provides a mapping between chromosome names between, eg |
| | UCSC, ensembl, etc. |
| | |
| | ## Usage |
| | |
| | Currently, we expect that this will be used for its raw files, eg by downloading a given |
| | file and opening it in your favorite program. |
| | |
