| --- |
| license: mit |
| language: |
| - en |
| tags: |
| - biology |
| - genomics |
| - yeast |
| - transcription-factors |
| - callingcards |
| - transposon |
| - binding |
| - gene-expression |
| pretty_name: "Calling Cards Transcription Factor Binding Dataset" |
|
|
| experimental_conditions: |
| temperature_celsius: room |
| media: |
| name: synthetic_complete_minus_ura_his_leu |
| carbon_source: |
| - compound: D-galactose |
| concentration_percent: 2 |
| nitrogen_source: |
| - compound: amino_acid_dropout_mix |
| concentration_percent: unspecified |
| specifications: |
| - minus_ura |
| - minus_his |
| - minus_leu |
| citation: Mateusiak, C, Erdenebaatar, Z, Jia, E, Plaggenberg, JN, Wang, Y, Shively, C, Liao, G, Mitra, RD, Brent, MR. 2026. Functional synergy partially explains why most transcription factor binding is non-functional. bioRxiv 2026. |
| doi: https://doi.org/10.64898/2026.01.19.700460 |
| configs: |
| - config_name: annotated_features |
| description: Calling Cards transcription factor binding data with enrichment scores and statistical significance |
| dataset_type: annotated_features |
| default: true |
| data_files: |
| - split: train |
| path: annotated_features/*/*.parquet |
| dataset_info: |
| features: |
| - name: id |
| dtype: string |
| description: Unique identifier for each binding measurement |
| - 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 |
| - name: target_locus_tag |
| dtype: string |
| description: Systematic gene name (ORF identifier) of the target gene |
| - name: target_symbol |
| dtype: string |
| description: Standard gene symbol of the target gene |
| - name: experiment_hops |
| dtype: float64 |
| description: Number of transposon insertion events (hops) at target locus in experimental sample |
| - name: background_hops |
| dtype: float64 |
| description: Number of transposon insertion events (hops) at target locus in background control |
| - name: background_total_hops |
| dtype: float64 |
| description: Total number of background hops across all loci in the control sample |
| - name: experiment_total_hops |
| dtype: float64 |
| description: Total number of experimental hops across all loci in the experimental sample |
| - name: callingcards_enrichment |
| dtype: float64 |
| description: Enrichment score calculated as ratio of normalized experimental to background hops |
| - name: poisson_pval |
| dtype: float64 |
| description: P-value from Poisson test for statistical significance of binding enrichment |
| - name: hypergeometric_pval |
| dtype: float64 |
| description: P-value from hypergeometric test for statistical significance of binding enrichment |
| - name: batch |
| dtype: string |
| description: Experimental batch identifier for controlling batch effects |
|
|
| - config_name: annotated_features_meta |
| description: Metadata for annotated features datasets including regulator informatioand data quality indicators |
| dataset_type: metadata |
| applies_to: ["annotated_features"] |
| data_files: |
| - split: train |
| path: annotated_features_meta.parquet |
| dataset_info: |
| features: |
| - name: db_id |
| dtype: string |
| description: Database identifier for the dataset |
| role: experimental_condition |
| - name: regulator_locus_tag |
| dtype: string |
| description: Systematic identifier for the regulatory factor |
| role: regulator_identifier |
| - name: regulator_symbol |
| dtype: string |
| description: Standard symbol for the regulatory factor |
| role: regulator_identifier |
| - name: data_usable |
| dtype: string |
| description: Indicator of whether the data is suitable for analysis |
| role: experimental_condition |
| - name: preferred_replicate |
| dtype: string |
| description: Boolean indicator for preferred biological replicate |
| role: experimental_condition |
| - name: batch |
| dtype: string |
| description: Experimental batch identifier |
| role: experimental_condition |
| - name: single_binding |
| dtype: int64 |
| description: Count or score for single binding events |
| role: quantitative_measure |
| - name: composite_binding |
| dtype: int64 |
| description: Count or score for composite binding events |
| role: quantitative_measure |
| - name: analysis_set |
| dtype: bool |
| description: >- |
| TRUE if this record is to be used for analysis. FALSE otherwise. |
| This was determined in 2025. Replicates needed `>=`3k hops and |
| DTO `<=` 0.01 in either kemmeren or hackett |
| - name: id |
| dtype: string |
| description: Unique identifier for the metadata record |
|
|
| - config_name: annotated_features_combined |
| description: >- |
| Calling Cards replicate data combined at the qbed (genome map) level, with enrichment |
| and significance called via callingCardsTools. Partitioned by genome_map_id_set, |
| where each partition corresponds to a set of combined replicate genome maps for |
| a single regulator. |
| dataset_type: annotated_features |
| data_files: |
| - split: train |
| path: annotated_features_combined/*/*.parquet |
| dataset_info: |
| partitioning: |
| enabled: true |
| partition_by: ["genome_map_id_set"] |
| path_template: "annotated_features_combined/genome_map_id_set={genome_map_id_set}/*.parquet" |
| features: |
| - name: genome_map_id_set |
| dtype: string |
| description: >- |
| Hyphen-delimited set of genome map IDs corresponding to the combined replicates for this |
| regulator (partition key) |
| - 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 |
| - name: experiment_hops |
| dtype: float64 |
| description: Number of transposon insertion events (hops) at target locus in the experimental sample |
| role: quantitative_measure |
| - name: background_hops |
| dtype: float64 |
| description: Number of transposon insertion events (hops) at target locus in the background control |
| role: quantitative_measure |
| - name: background_total_hops |
| dtype: float64 |
| description: Total number of background hops across all loci in the control sample |
| role: quantitative_measure |
| - name: experiment_total_hops |
| dtype: float64 |
| description: Total number of experimental hops across all loci in the experimental sample |
| role: quantitative_measure |
| - name: callingcards_enrichment |
| dtype: float64 |
| description: Enrichment score calculated as ratio of normalized experimental to background hops |
| role: quantitative_measure |
| - name: poisson_pval |
| dtype: float64 |
| description: P-value from Poisson test for statistical significance of binding enrichment |
| role: quantitative_measure |
| - name: hypergeometric_pval |
| dtype: float64 |
| description: P-value from hypergeometric test for statistical significance of binding enrichment |
| role: quantitative_measure |
|
|
| - config_name: annotated_features_combined_meta |
| description: Sample-level metadata for combined Calling Cards experiments including regulator information, QC flags, and experimental conditions |
| dataset_type: metadata |
| applies_to: ["annotated_features_combined"] |
| data_files: |
| - split: train |
| path: annotated_features_combined_meta.parquet |
| dataset_info: |
| features: |
| - name: genome_map_id_set |
| dtype: string |
| description: Hyphen-delimited set of genome map IDs used as the partition key in annotated_features_combined |
| - name: pss_id |
| dtype: string |
| description: Passing sample set identifier grouping replicates used in this combined analysis |
| - name: binding_id |
| dtype: string |
| description: Unique identifier for this combined binding measurement record |
| - name: regulator_locus_tag |
| dtype: string |
| description: Systematic gene identifier for the transcription factor |
| role: regulator_identifier |
| - name: regulator_symbol |
| dtype: string |
| description: Standard gene symbol for the transcription factor |
| role: regulator_identifier |
| - name: batch |
| dtype: string |
| description: Experimental batch identifier for controlling batch effects |
| - name: analysis_set |
| dtype: bool |
| description: >- |
| For a TF with more than 1 passing replicate, a combined samples is created. |
| This is based on the QC done in 2025 for the modeling paper. See the |
| annotated_features_meta for more details |
| - name: condition |
| dtype: string |
| description: Experimental condition for this sample |
| role: experimental_condition |
|
|
| - config_name: 2026_analysis_set |
| description: >- |
| This is a combination of the combined annotated_features_combined dataset, and the |
| passing single replicates from the annotated_features dataset. This is the data |
| that is used for the 2026 modeling paper as predictors |
| dataset_type: annotated_features |
| metadata_fields: ["gm_id","regulator_locus_tag","regulator_symbol", "experiment_total_hops", "background_total_hops"] |
| data_files: |
| - split: train |
| path: 2026_analysis_set.parquet |
| dataset_info: |
| features: |
| - name: gm_id |
| dtype: string |
| description: >- |
| genome_map id. If the sample is a combination of multiple samples, then it is a |
| hyphen-delimited set of genome map IDs corresponding to the combined replicates for this |
| regulator. |
| - 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 |
| - name: experiment_hops |
| dtype: float64 |
| description: Number of transposon insertion events (hops) at target locus in the experimental sample |
| role: quantitative_measure |
| - name: background_hops |
| dtype: float64 |
| description: Number of transposon insertion events (hops) at target locus in the background control |
| role: quantitative_measure |
| - name: background_total_hops |
| dtype: float64 |
| description: Total number of background hops across all loci in the control sample |
| role: quantitative_measure |
| - name: experiment_total_hops |
| dtype: float64 |
| description: Total number of experimental hops across all loci in the experimental sample |
| role: quantitative_measure |
| - name: callingcards_enrichment |
| dtype: float64 |
| description: Enrichment score calculated as ratio of normalized experimental to background hops |
| role: quantitative_measure |
| - name: poisson_pval |
| dtype: float64 |
| description: P-value from Poisson test for statistical significance of binding enrichment |
| role: quantitative_measure |
|
|
| - config_name: genome_map |
| description: Genome-wide calling cards insertion density data partitioned by batch |
| dataset_type: genome_map |
| data_files: |
| - split: train |
| path: genome_map/*/*.parquet |
| dataset_info: |
| features: |
| - name: id |
| dtype: string |
| description: Unique identifier for each genomic interval |
| - name: chr |
| dtype: string |
| description: Chromosome name (e.g., chrI, chrII, etc.) |
| - name: start |
| dtype: float64 |
| description: Start position of genomic interval |
| - name: end |
| dtype: float64 |
| description: End position of genomic interval |
| - name: depth |
| dtype: float64 |
| description: Number of transposon insertion events (read depth) in this genomic interval |
| - name: strand |
| dtype: string |
| description: Strand information (+ or -) for the genomic interval |
| - name: batch |
| dtype: string |
| description: Experimental batch identifier |
| partitioning: |
| enabled: true |
| partition_by: ["batch"] |
| path_template: "genome_map/batch={batch}/*.parquet" |
|
|
| - config_name: genome_map_meta |
| description: Metadata for genome map datasets including regulator information and experimental details |
| dataset_type: metadata |
| applies_to: ["genome_map", "annotated_features_orig_reprocess"] |
| data_files: |
| - split: train |
| path: genome_map_meta.parquet |
| dataset_info: |
| features: |
| - name: id |
| dtype: string |
| description: Unique identifier for the metadata record |
| - name: binding_id |
| dtype: string |
| description: current django managed database identifier for the dataset to the 'binding' table |
| - name: regulator_locus_tag |
| dtype: string |
| description: Systematic identifier for the regulatory factor |
| role: regulator_identifier |
| - name: regulator_symbol |
| dtype: string |
| description: Standard symbol for the regulatory factor |
| role: regulator_identifier |
| - name: batch |
| dtype: string |
| description: Experimental batch identifier |
| role: experimental_condition |
| - name: replicate |
| dtype: int64 |
| description: Biological replicate number, within batch |
| - name: notes |
| dtype: string |
| description: Additional notes or comments about the experiment |
| - name: condition |
| dtype: |
| class_label: |
| names: [ |
| "standard", "rapa", "starvation", "glu_1_gal_1", |
| "del_MET28", "glu_1_gal_2", "del_FKH2", "del_TYE7" |
| ] |
| description: >- |
| Experimental condition of the sample, including standard growth, rapamycin treatment, |
| nutrient starvation, mixed carbon source conditions, and gene deletion strains |
| role: experimental_condition |
| definitions: |
| standard: |
| media: |
| name: synthetic_complete |
| carbon_source: |
| - compound: D-glucose |
| concentration_percent: 2 |
| rapa: |
| perturbation_method: |
| type: chemical_treatment |
| compound: rapamycin |
| description: Rapamycin treatment to inhibit TORC1 signaling |
| starvation: |
| description: "Nutrient starvation condition - specific media composition not defined in source" |
| glu_1_gal_1: |
| media: |
| carbon_source: |
| - compound: D-glucose |
| concentration_percent: 1 |
| - compound: D-galactose |
| concentration_percent: 1 |
| glu_1_gal_2: |
| media: |
| carbon_source: |
| - compound: D-glucose |
| concentration_percent: 1 |
| - compound: D-galactose |
| concentration_percent: 2 |
| del_MET28: |
| genotype: |
| deletions: |
| - gene: MET28 |
| description: MET28 deletion strain |
| del_FKH2: |
| genotype: |
| deletions: |
| - gene: FKH2 |
| description: FKH2 deletion strain |
| del_TYE7: |
| genotype: |
| deletions: |
| - gene: TYE7 |
| description: TYE7 deletion strain |
|
|
| - config_name: annotated_features_orig_reprocess |
| description: >- |
| Calling Cards annotated features reprocessed from the original qbed genome maps |
| using scripts/quantify_regions.R. Each record corresponds to a single genome map |
| (replicate-level), where the id field links to genome_map_meta. Includes log-transformed |
| p-values and FDR-adjusted q-values not present in the original annotated_features_combined. |
| dataset_type: annotated_features |
| data_files: |
| - split: train |
| path: annotated_features_orig_reprocess/*/*.parquet |
| dataset_info: |
| features: |
| - name: id |
| dtype: int64 |
| description: Genome map identifier linking to the genome_map and genome_map_meta dataset |
| - 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 |
| - name: experiment_hops |
| dtype: float64 |
| description: Number of transposon insertion events (hops) at target locus in the experimental sample |
| role: quantitative_measure |
| - name: background_hops |
| dtype: float64 |
| description: Number of transposon insertion events (hops) at target locus in the background control |
| role: quantitative_measure |
| - name: total_background_hops |
| dtype: float64 |
| description: Total number of background hops across all loci in the control sample |
| role: quantitative_measure |
| - name: total_experiment_hops |
| dtype: float64 |
| description: Total number of experimental hops across all loci in the experimental sample genomic (not mito) chromosomes |
| role: quantitative_measure |
| - name: callingcards_enrichment |
| dtype: float64 |
| description: Enrichment score calculated as ratio of normalized experimental to background hops |
| role: quantitative_measure |
| - name: poisson_pval |
| dtype: float64 |
| description: P-value from Poisson test for statistical significance of binding enrichment |
| role: quantitative_measure |
| - name: log_poisson_pval |
| dtype: float64 |
| description: Log-transformed Poisson p-value. This has greater numeric resolution for significant loci |
| role: quantitative_measure |
| - name: poisson_qval |
| dtype: float64 |
| description: FDR-adjusted q-value from Poisson test (multiple testing correction) |
| role: quantitative_measure |
| - name: hypergeometric_pval |
| dtype: float64 |
| description: P-value from hypergeometric test for statistical significance of binding enrichment |
| role: quantitative_measure |
| - name: log_hypergeometric_pval |
| dtype: float64 |
| description: Log-transformed hypergeometric p-value |
| role: quantitative_measure |
| - name: hypergeometric_qval |
| dtype: float64 |
| description: FDR-adjusted q-value from hypergeometric test (multiple testing correction) |
| role: quantitative_measure |
| - name: batch |
| dtype: string |
| description: Experimental batch identifier for controlling batch effects (parition key) |
| --- |
| # Calling Cards |
|
|
| This is data produced in both the Brent Lab and Mitra Lab at Washington University |
|
|
| This repo provides 2 dataset and associated metadata: |
|
|
| - **annotated_features**: This data scores promoter regions associated with the nearest gene |
| - **genome_map**: The binding location data in qbed format |
|
|
| In the annotated features, in order to get the analysis set (you can use duckdb directory instead |
| of `tfbpapi` -- see the usage section below): |
|
|
| ```python |
| import pandas as pd |
| from tfbpapi.HfQueryAPI import HfQueryAPI |
| |
| # Initialize the Hugging Face query API with the calling cards dataset |
| callingcards_hf = HfQueryAPI( |
| repo_id="BrentLab/callingcards", |
| repo_type="dataset" |
| ) |
| |
| # Set a filter to only include records where data quality passes QC |
| callingcards_hf.set_filter("annotated_features", data_usable="pass") |
| |
| # Query all columns from the annotated_features table |
| # Returns the data as a pandas DataFrame |
| callingcards_data = callingcards_hf.query( |
| "SELECT * FROM annotated_features", |
| "annotated_features" |
| ) |
| |
| analysis_data = ( |
| callingcards_data |
| .assign( |
| # Create a flag: does this regulator have any composite binding? |
| has_composite = lambda df: df.groupby('regulator_locus_tag')['composite_binding'] |
| .transform(lambda x: x.notna().any()) |
| ) |
| .query( |
| # If composite exists for this regulator, require composite to be non-null |
| # Otherwise, require single_binding to be non-null |
| '(has_composite & composite_binding.notna()) | ' |
| '(~has_composite & single_binding.notna())' |
| ) |
| .drop(columns=['has_composite']) # Remove the helper column |
| ) |
| ``` |
|
|
| ## Usage |
|
|
| The python package `tfbpapi` provides an interface to this data which eases |
| examining the datasets, field definitions and other operations. You may also |
| download the parquet datasets directly from hugging face by clicking on |
| "Files and Versions", or by using the huggingface_cli and duckdb directly. |
| In both cases, this provides a method of retrieving dataset and field definitions. |
| |
| ### `tfbpapi` |
| |
| After [installing |
| tfbpapi](https://github.com/BrentLab/tfbpapi/?tab=readme-ov-file#installation), you can |
| adapt this [tutorial](https://brentlab.github.io/tfbpapi/tutorials/hfqueryapi_tutorial/) |
| in order to explore the contents of this repository. |
| |
| ### huggingface_cli/duckdb |
|
|
| You can retrieves and displays the file paths for each configuration of |
| the "BrentLab/callingcards" dataset from Hugging Face Hub. |
|
|
| ```python |
| from huggingface_hub import ModelCard |
| from pprint import pprint |
| |
| card = ModelCard.load("BrentLab/callingcards", repo_type="dataset") |
| |
| # cast to dict |
| card_dict = card.data.to_dict() |
| |
| # Get partition information |
| dataset_paths_dict = {d.get("config_name"): d.get("data_files")[0].get("path") for d in card_dict.get("configs")} |
| |
| pprint(dataset_paths_dict) |
| ``` |
|
|
| The entire repository is large. It may be preferable to only retrieve |
| specific files or partitions. You can use the metadata files to choose |
| which files to pull. |
|
|
| ```python |
| from huggingface_hub import snapshot_download |
| import duckdb |
| import os |
| # Download only the metadata first |
| repo_path = snapshot_download( |
| repo_id="BrentLab/callingcards", |
| repo_type="dataset", |
| allow_patterns="annotated_features_meta.parquet" |
| ) |
| |
| dataset_path = os.path.join(repo_path, "annotated_features_meta.parquet") |
| conn = duckdb.connect() |
| meta_res = conn.execute("SELECT * FROM read_parquet(?) LIMIT 10", [dataset_path]).df() |
| print(meta_res) |
| ``` |
|
|
| We might choose to take a look at the file with id = 1: |
|
|
| ```python |
| # Download only a specific sample's genome coverage data |
| repo_path = snapshot_download( |
| repo_id="BrentLab/callingcards", |
| repo_type="dataset", |
| allow_patterns="annotated_features/id=1/*.parquet" |
| ) |
| |
| # Query the specific partition |
| dataset_path = os.path.join(repo_path, "annotated_features") |
| result = conn.execute("SELECT * FROM read_parquet(?) LIMIT 10", |
| [f"{dataset_path}/**/*.parquet"]).df() |
| print(result) |
| ``` |
|
|
| If you wish to pull the entire repo, due to its size you may need to use an |
| [authentication token](https://huggingface.co/docs/hub/en/security-tokens). |
| If you do not have one, try omitting the token related code below and see if |
| it works. Else, create a token and provide it like so: |
|
|
| ```python |
| |
| repo_id = "BrentLab/callingcards" |
| |
| hf_token = os.getenv("HF_TOKEN") |
| |
| # Download entire repo to local directory |
| repo_path = snapshot_download( |
| repo_id=repo_id, |
| repo_type="dataset", |
| token=hf_token |
| ) |
| |
| print(f"\n✓ Repository downloaded to: {repo_path}") |
| |
| # Construct path to the annotated_features_meta parquet file |
| parquet_path = os.path.join(repo_path, "annotated_features_meta.parquet") |
| print(f"✓ Parquet file at: {parquet_path}") |
| |
