--- license: mit tags: - transcription-factor - binding - chipexo - genomics - biology language: - en pretty_name: Rossi ChIP-exo 2021 experimental_conditions: temperature_celsius: 25 cultivation_method: unspecified growth_phase_at_harvest: phase: mid_log od600: 0.8 media: name: yeast_peptone_dextrose carbon_source: - compound: D-glucose concentration_percent: unspecified nitrogen_source: - compound: yeast_extract concentration_percent: unspecified - compound: peptone concentration_percent: unspecified # Heat shock applied only to SAGA strains # note that im not sure which strains this # applies to -- it is a TODO to better # document this heat_shock: induced: true temperature_celsius: 37 duration_minutes: 6 pre_induction_temperature_celsius: 25 method: equal_volume_medium_transfer doi: https://doi.org/10.1038/s41586-021-03314-8 citation: Rossi, MJ, Kuntala, PK, Lai, WKM, Yamada, N, Badjatia, N, Mittal, et al. 2021. A high-resolution protein architecture of the budding yeast genome. Nature. features: - applies_to: - rossi_2021_metadata_replicate - rossi_2021_metadata_sample fields: - name: treatment dtype: string description: >- Experimental treatment applied prior to ChIP-exo. The majority of samples are untreated; a subset of SAGA-associated factors received a brief heat shock (equal volume of 37°C medium mixed into a 25°C culture, 6 min at 37°C). role: experimental_condition - name: growth_media dtype: string description: >- Growth medium used in the experiment, as reported in yeastepigenome.org sample metadata. The majority of samples used YPD (rich medium). role: experimental_condition - applies_to: - rossi_2021_metadata_replicate - rossi_2021_metadata_sample - rossi_2021_af_replicates - rossi_2021_af_combined - rossi_2021_af_replicates_mindel - rossi_2021_af_combined_mindel - rossi_2021_af_start_codon_500bp_replicates - rossi_2021_af_combined_start_codon_500bp - rossi_2021_af_replicates_intergenic_replicates - rossi_2021_af_combined_intergenic fields: - name: regulator_locus_tag dtype: string description: Systematic gene name (ORF identifier) of the transcription factor - name: regulator_symbol dtype: string description: Standard gene symbol of the transcription factor - applies_to: - macs_bp500 - macs_intergenic - macs_kang - macs_mindel fields: - name: n_peaks dtype: int32 description: number of peaks that are annotated to within 700 bp of the target. Note that a peak may be annotated to multiple targets - name: nearest_score dtype: float64 description: -log10(qvalue) of the peak nearest to the target - name: median_score dtype: float64 description: median -log10(qvalue) of the peaks annotated to the target - name: max_score dtype: float64 description: max -log10(qvalue) of the peaks annotated to the target - applies_to: - rossi_2021_af_replicates - rossi_2021_af_combined - rossi_2021_af_replicates_mindel - rossi_2021_af_combined_mindel - yep_filtered_peaks_combined - rossi_2021_af_start_codon_500bp_replicates - rossi_2021_af_combined_start_codon_500bp - rossi_2021_af_replicates_intergenic_replicates - rossi_2021_af_combined_intergenic - macs_bp500 - macs_intergenic - macs_kang - macs_mindel fields: - name: target_locus_tag dtype: string description: Systematic gene identifier for the target gene role: target_identifier - name: target_symbol dtype: string description: Standard gene symbol for the target gene role: target_identifier - applies_to: - rossi_2021_af_replicates - rossi_2021_af_combined - rossi_2021_af_replicates_mindel - rossi_2021_af_combined_mindel - rossi_2021_af_start_codon_500bp_replicates - rossi_2021_af_combined_start_codon_500bp - rossi_2021_af_replicates_intergenic_replicates - rossi_2021_af_combined_intergenic fields: - name: seqnames dtype: string description: Chromosome identifier (e.g., chrI, chrII, chrXVI) - name: start dtype: int64 description: Promoter region start position (1-based coordinate) - name: end dtype: int64 description: Promoter region end position (1-based, inclusive) - applies_to: - rossi_2021_af_replicates - rossi_2021_af_combined - rossi_2021_af_replicates_mindel - rossi_2021_af_combined_mindel - rossi_2021_af_start_codon_500bp_replicates - rossi_2021_af_combined_start_codon_500bp - rossi_2021_af_replicates_intergenic_replicates - rossi_2021_af_combined_intergenic fields: - name: background_counts dtype: float64 description: Read counts in the background/control sample for this peak region role: quantitative_measure - name: experiment_counts dtype: float64 description: Read counts in the ChIP-exo experiment sample for this peak region role: quantitative_measure - name: total_background_counts dtype: int64 description: Total read counts across the entire genome in the background sample role: quantitative_measure - name: total_experiment_counts dtype: int64 description: Total read counts across the entire genome in the experiment sample role: quantitative_measure - name: enrichment dtype: float64 description: Enrichment score for the binding peak role: quantitative_measure - name: poisson_pval dtype: float64 description: P-value from Poisson distribution test for peak significance role: quantitative_measure - name: log_poisson_pval dtype: float64 description: Log-transformed Poisson p-value role: quantitative_measure - name: hypergeometric_pval dtype: float64 description: P-value from hypergeometric distribution test for peak significance role: quantitative_measure - name: log_hypergeometric_pval dtype: float64 description: Log-transformed hypergeometric p-value role: quantitative_measure - name: poisson_qval dtype: float64 description: FDR-adjusted q-value from Poisson test (multiple testing correction) role: quantitative_measure - name: hypergeometric_qval dtype: float64 description: FDR-adjusted q-value from hypergeometric test (multiple testing correction) role: quantitative_measure - applies_to: - rossi_2021_af_replicates_intergenic_replicates - rossi_2021_af_combined_intergenic fields: - name: ir_name dtype: string description: >- Unique identifier of the intergenic region. See yeast_genome_resources/intergenic_regions_metadata_5_1.csv for details on the region (location, etc). Note that these intergenic regions are defined as the region between the end of one ORF and the start of the next, and are named according to the locus tags of the flanking ORFs (e.g., YAL001C-YAL002W). A intergenic region is assigned to a promoter only when the 5' end is continuous with the region. - applies_to: - rossi_2021_af_replicates_mindel - rossi_2021_af_combined_mindel fields: - name: width dtype: int64 description: Width of the promoter region - name: strand dtype: string description: Genomic strand of the promoter region (+ or -) - name: mindel_name dtype: string description: Name of the promoter region as defined in the Mindel promoters - name: promoter_sequence dtype: string description: Nucleotide sequence of the promoter region - name: in_mahendrawada_features dtype: bool description: >- TRUE if the promoter region was used in Mahendrawada 2025. Note that this is equivalent to protein coding non dubious ORF - name: promoter_exact_aligns dtype: int64 description: >- this is a feature from the Mindel data that I have not documented. It is a TODO. - applies_to: - yep_filtered_peaks_combined fields: - name: peak_score dtype: float64 description: >- The filtered bed file representing the high confidence ChExMix peaks from yeastepigenome.org score. Where multiple peaks are within 500bp upstream of a target ORF, we take the median peak score. Replicates are then combined. When combining replicates, the median score across all replicates is taken. - name: n_peaks dtype: int32 description: >- The number of peaks annotated to the same target. This is both within replicates and across (ie, there might be 3 peaks in 2 replicates for a total of 6 in this data) - name: max_distance dtype: float64 description: >- The maximum distance a peak in the set (see n_peaks) is from the ORF - name: peak_n_replicates dtype: int32 description: >- The number of replicates which have peaks for this target configs: - config_name: rossi_2021_metadata_replicate description: Metadata describing the tagged regulator in each experiment dataset_type: metadata applies_to: ["genome_map", "yep_filtered_peaks"] data_files: - split: train path: rossi_2021_metadata.parquet dataset_info: features: - name: accession dtype: string description: GEO run accession identifier for the sample role: sample_id - name: sample_id dtype: int64 description: >- Unique identifier for the biological replicate. Note this is the same as the sample_id in rossi_2021_metadata_sample - name: yeastepigenome_id dtype: float64 description: Sample identifier used by yeastepigenome.org - name: antibody dtype: string description: Antibody used for ChIP-exo immunoprecipitation - config_name: rossi_2021_metadata_sample description: Sample-level metadata for combined ChIP-exo experiments including experimental conditions dataset_type: metadata applies_to: ["rossi_2021_af_combined", "rossi_2021_af_combined_mindel", "yep_filtered_peaks_combined", "rossi_2021_af_combined_start_codon_500bp", "rossi_2021_af_combined_intergenic", "macs_bp500", "macs_intergenic", "macs_kang", "macs_mindel"] data_files: - split: train path: rossi_2021_metadata_sample.parquet dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier combining regulator and replicates - name: multi_antibody dtype: bool description: TRUE if the set of replicates includes more than one type of antibody - name: antibody dtype: string description: >- Antibody used for ChIP-exo immunoprecipitation. If multi_antibody is TRUE, then the antibodies in the set are separated by `;` - config_name: genome_map_control_meta description: Sample accession metadata for ChIP-exo input/control coverage tracks dataset_type: metadata applies_to: ["genome_map_control"] data_files: - split: train path: genome_map_control_meta.parquet dataset_info: features: - name: accession dtype: string description: SRA run accession identifier for the control sample - name: yeastepigenome_id dtype: float64 description: Sample identifier used by yeastepigenome.org - config_name: genome_map description: >- ChIP-exo 5' tag coverage data partitioned by sample accession. See https://github.com/BrentLab/checseq_promoter_enrichment_slurm_pipeline/tree/main/promoter_enrichment for how these are created from alignments. dataset_type: genome_map data_files: - split: train path: genome_map/*/*.parquet partitioning: enabled: true partition_by: ["accession"] path_template: "genome_map/accession={accession}/*.parquet" dataset_info: features: - name: accession dtype: string description: GEO run accession identifier for the sample (partitioning column) - name: chr dtype: string description: Chromosome name (e.g., chrI, chrII, etc.) - name: pos dtype: int32 description: "Genomic position of the 5' tag" - name: pileup dtype: int32 description: "Depth of coverage (number of 5' tags) at this genomic position" - config_name: genome_map_control description: "ChIP-exo 5' tag coverage data for input/control samples, partitioned by sample accession" dataset_type: genome_map data_files: - split: train path: genome_map_control/*/*.parquet partitioning: enabled: true partition_by: ["accession"] path_template: "genome_map_control/accession={accession}/*.parquet" dataset_info: features: - name: accession dtype: string description: GEO run accession identifier for the sample (partitioning column) - name: chr dtype: string description: Chromosome name (e.g., chrI, chrII, etc.) - name: pos dtype: int32 description: "Genomic position of the 5' tag" - name: pileup dtype: int32 description: "Depth of coverage (number of 5' tags) at this genomic position" - config_name: yep_filtered_peaks description: "yeastepigenome.org peaks with the peaks overlapping blacklisted regions removed (see Rossi paper)" dataset_type: genome_map data_files: - split: train path: yep_filtered_peaks.parquet dataset_info: features: - name: yeastepigenome_id dtype: string description: Sample identifier used by yeastepigenome.org - name: chr dtype: string description: Chromosome name (e.g., chrI, chrII, etc.) - name: start dtype: float64 description: 0-based start position of the peak region - name: end dtype: float64 description: 0-based, half open end position of a single base resolution peak - name: score dtype: float64 description: "Score assigned by ChExMix as reported by yeastepigenome.org" - config_name: macs_bp500 description: >- peaks called with macs. see scripts/rossi_peak_analysis.R for details. then intersected with the promoter set defined as 500 bp upstream of the start codon. dataset_type: annotated_features data_files: - split: train path: macs_bp500.parquet genome_resources: region_sets: start_codon_500bp: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/start_codon_500bp_upstream_promoters.bed join_column: target_locus_tag dataset_info: features: - name: sample_id dtype: int64 description: sample identifier. use with rossi_2021_metadata_sample - config_name: macs_intergenic description: >- peaks called with macs. see scripts/rossi_peak_analysis.R for details. then intersected with the promoter set defined as the intergenic regions from SGD 5-1. dataset_type: annotated_features data_files: - split: train path: macs_intergenic.parquet genome_resources: region_sets: intergenic: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/intergenic_regions_metadata_5_1.csv join_column: target_locus_tag dataset_info: features: - name: sample_id dtype: int64 description: sample identifier. use with rossi_2021_metadata_sample - config_name: macs_kang description: >- peaks called with macs. see scripts/rossi_peak_analysis.R for details. then intersected with the promoter set defined as 700 bp upstream, truncated by upstream features. dataset_type: annotated_features data_files: - split: train path: macs_kang.parquet genome_resources: region_sets: Kang: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/yiming_promoters.bed join_column: target_locus_tag dataset_info: features: - name: sample_id dtype: int64 description: sample identifier. use with rossi_2021_metadata_sample - config_name: macs_mindel description: >- peaks called with macs. see scripts/rossi_peak_analysis.R for details. then intersected with the promoter set defined by Mindel. See huggingface/BrentLab/yeast_genome_resources. dataset_type: annotated_features data_files: - split: train path: macs_mindel.parquet genome_resources: region_sets: Mindel: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/mindel_promoters.csv.gz join_column: target_locus_tag dataset_info: features: - name: sample_id dtype: int64 description: sample identifier. use with rossi_2021_metadata_sample - config_name: rossi_2021_af_replicates description: ChIP-exo annotated features at biological replicate level with binding peaks and statistical significance metrics dataset_type: annotated_features genome_resources: region_sets: Kang: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/yiming_promoters.bed join_column: target_locus_tag data_files: - split: train path: rossi_2021_af_replicates.parquet dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier for the biological replicate role: sample_id - name: run_accession dtype: string description: SRA run accession identifier for this biological replicate - config_name: rossi_2021_af_replicates_mindel description: ChIP-exo annotated features at biological replicate level with binding peaks and statistical significance metrics dataset_type: annotated_features genome_resources: region_sets: Mindel: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/mindel_promoters.csv.gz join_column: target_locus_tag data_files: - split: train path: rossi_2021_af_replicates_mindel.parquet dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier for the biological replicate role: sample_id - name: run_accession dtype: string description: SRA run accession identifier for this biological replicate - config_name: rossi_2021_af_start_codon_500bp_replicates description: ChIP-exo annotated features at biological replicate level with binding scores and statistical significance metrics for promoter regions defined as 500bp upstream of the start codon dataset_type: annotated_features genome_resources: region_sets: start_codon_500bp: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/start_codon_500bp_upstream_promoters.bed join_column: target_locus_tag data_files: - split: train path: rossi_2021_af_start_codon_500bp_replicates.parquet dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier for the biological replicate role: sample_id - name: accession dtype: string description: SRA run accession identifier for this biological replicate - config_name: rossi_2021_af_replicates_intergenic_replicates description: ChIP-exo annotated features at biological replicate level with binding scores and statistical significance metrics for intergenic regions. dataset_type: annotated_features genome_resources: region_sets: intergenic: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/intergenic_regions_metadata_5_1.csv join_column: ir_name data_files: - split: train path: rossi_2021_af_intergenic_replicates.parquet dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier for the biological replicate role: sample_id - name: accession dtype: string description: SRA run accession identifier for this biological replicate - config_name: rossi_2021_af_combined description: Combined ChIP-exo annotated features with binding peaks and statistical significance metrics aggregated across biological replicates dataset_type: annotated_features genome_resources: region_sets: Kang: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/yiming_promoters.bed join_column: target_locus_tag data_files: - split: train path: rossi_2021_af_combined.parquet dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier combining regulator and replicates role: sample_id - config_name: rossi_2021_af_combined_mindel description: >- Combined ChIP-exo annotated features with binding peaks and statistical significance metrics aggregated across biological replicates dataset_type: annotated_features genome_resources: region_sets: Mindel: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/mindel_promoters.csv.gz join_column: target_locus_tag data_files: - split: train path: rossi_2021_af_combined_mindel.parquet dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier combining regulator and replicates role: sample_id - config_name: yep_filtered_peaks_combined description: >- The filtered high confidence peaks reported at yeastepigenome.org. The peaks are annotated to the nearest downstream gene (not dubious). Peaks within 500 bp of the ORF are keep. Within a given replicate, if a target has more than 1 peak, then the median score is taken. Replicates are combined in the same way, with the median target score across replicates. see `scripts/parse_rossi_filtered_peaks.R` for more details. data_files: - split: train path: yep_filtered_peaks_combined.parquet dataset_type: annotated_features dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier for the biological replicate role: sample_id - config_name: rossi_2021_af_combined_intergenic description: >- Combined ChIP-exo annotated features with binding score and statistical significance metrics aggregated across biological replicates. Binding peaks are annotated to intergenic regions as defined in yeast_genome_resources/intergenic_regions_metadata_5_1.csv. Note that these intergenic regions are defined as the region between the end of one ORF and the start of the next, and are named according to the locus tags of the flanking ORFs (e.g., YAL001C-YAL002W). A intergenic region is assigned to a promoter only when the 5' end is continuous with the region. dataset_type: annotated_features genome_resources: region_sets: intergenic: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/intergenic_regions_metadata_5_1.csv join_column: ir_name data_files: - split: train path: rossi_2021_af_intergenic_combined.parquet dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier combining regulator and replicates role: sample_id - config_name: rossi_2021_af_combined_start_codon_500bp description: >- Combined ChIP-exo annotated features with binding score and statistical significance metrics aggregated across biological replicates for promoter regions defined as 500bp upstream of the start codon. Binding peaks are annotated to these promoter regions as defined in yeast_genome_resources/start_codon_500bp_upstream_promoters.bed. dataset_type: annotated_features genome_resources: region_sets: start_codon_500bp: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/start_codon_500bp_upstream_promoters.bed join_column: target_locus_tag data_files: - split: train path: rossi_2021_af_start_codon_500bp_combined.parquet dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier combining regulator and replicates role: sample_id --- # Rossi 2021 This data is gathered from [yeastepigenome.org](https://yeastepigenome.org/). This work was published in [Rossi MJ, Kuntala PK, Lai WKM, Yamada N, Badjatia N, Mittal C, Kuzu G, Bocklund K, Farrell NP, Blanda TR, Mairose JD, Basting AV, Mistretta KS, Rocco DJ, Perkinson ES, Kellogg GD, Mahony S, Pugh BF. A high-resolution protein architecture of the budding yeast genome. Nature. 2021 Apr;592(7853):309-314. doi: 10.1038/s41586-021-03314-8. Epub 2021 Mar 10. PMID: 33692541; PMCID: PMC8035251.](https://doi.org/10.1038/s41586-021-03314-8) ## Accessing Data The examples below require [labretriever](https://github.com/cmatKhan/labretriever#installation) (`pip install labretriever`) and/or the [HuggingFace Hub client](https://huggingface.co/docs/huggingface_hub/installation) (`pip install huggingface_hub`). ### Accessing Data with labretriever This repository is part of a collection configured as a unified database using [labretriever.VirtualDB](https://cmatkhan.github.io/labretriever/virtual_db_configuration/). Download the [collection config](https://github.com/BrentLab/tfbpshiny/blob/main/tfbpshiny/brentlab_yeast_collection.yaml) and use it to query the data directly in Python, or with an AI assistant using the [labretriever plugin](https://cmatkhan.github.io/labretriever/mcp_server/#quick-install-claude-code-plugin). ```python from labretriever.virtual_db import VirtualDB from labretriever.datacard import DataCard # Citation and metadata card = DataCard("BrentLab/rossi_2021") info = card.info() print(info["doi"]) print(info["citation"]) # path to the downloaded brentlab_yeast_collection.yaml vdb = VirtualDB("/path/to/brentlab_yeast_collection.yaml") print(vdb.get_dataset_description("rossi")) vdb.query("SELECT * FROM rossi LIMIT 5") ``` ### Direct parquet access The repository contains more data than what is exposed through the collection configuration. Use `DataCard.info()` to inspect available files, then download and query with DuckDB. Most files in this repository are single parquet files and can be read directly: ```python from huggingface_hub import snapshot_download import duckdb repo_path = snapshot_download( repo_id="BrentLab/rossi_2021", repo_type="dataset", allow_patterns="rossi_2021_af_combined.parquet", ) conn = duckdb.connect() # returns a pandas DataFrame with the first 5 rows conn.execute( "SELECT * FROM read_parquet(?) LIMIT 5", [f"{repo_path}/rossi_2021_af_combined.parquet"], ).df() ``` ### Accessing using R Clone the repository and read parquet files directly with [arrow](https://arrow.apache.org/docs/r/): ```r # install.packages("arrow") arrow::read_parquet("rossi_2021_af_combined.parquet") ```