metadata
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:
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. This work was published in
Accessing Data
The examples below require
labretriever
(pip install labretriever) and/or the
HuggingFace Hub client
(pip install huggingface_hub).
Accessing Data with labretriever
This repository is part of a collection configured as a unified database using labretriever.VirtualDB. Download the collection config and use it to query the data directly in Python, or with an AI assistant using the labretriever plugin.
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:
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:
# install.packages("arrow")
arrow::read_parquet("rossi_2021_af_combined.parquet")