Update README.md

README.md

@@ -1,3 +1,282 @@
----
-license: mit
----
+---
+license: mit
+language:
+- en
+tags:
+- biology
+- genomics
+- yeast
+- transcription-factors
+- gene-expression
+- binding
+- chec
+- perturbation
+- rnaseq
+- nascent rnaseq
+pretty_name: "Mahendrawada 2025 ChEC-seq and Nascent RNA-seq data"
+size_categories:
+- 100K<n<1M
+configs:
+- config_name: genomic_features
+  description: Comprehensive genomic features and regulatory characteristics for yeast genes
+  data_files:
+  - split: train
+    path: features_mahendrawada_2025.parquet
+  dataset_info:
+    features:
+    - name: gene_id
+      dtype: string
+      description: Systematic gene name (ORF identifier) from SGD (https://yeastgenome.org/)
+    - name: SGD_id
+      dtype: string
+      description: Unique identifier for each gene from SGD (https://yeastgenome.org/)
+    - name: gene_name
+      dtype: string
+      description: Common name of each gene
+    - name: chr
+      dtype: string
+      description: Chromosome number corresponding to gene
+    - name: strand
+      dtype: string
+      description: Strandedness of the gene (+ or -)
+    - name: start
+      dtype: int64
+      description: Start position of the ORF
+    - name: end
+      dtype: int64
+      description: End position of the ORF
+    - name: TSS
+      dtype: int64
+      description: Transcription start site based on Park et al., 2014 (doi:10.1093/nar/gkt1366)
+    - name: TATA_category
+      dtype: string
+      description: TATA box classification from Donczew et al., 2020 using consensus TATAWAW (doi:10.7554/eLife.50109)
+    - name: expression
+      dtype: float64
+      description: Average signal normalized to gene length from Donczew et al., 2020 (doi:10.7554/eLife.50109)
+    - name: +1 nucleosome
+      dtype: float64
+      description: Position of +1 nucleosome from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)
+    - name: -1 nucleosome
+      dtype: float64
+      description: Position of -1 nucleosome from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)
+    - name: NDR Center
+      dtype: float64
+      description: Center of nucleosome depleted region from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)
+    - name: NDR Width
+      dtype: float64
+      description: Width of nucleosome depletion region from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)
+    - name: tail-dependence
+      dtype: string
+      description: Tail classification based on Mediator tail dependence from Warfield L, Donczew R et al., 2022 (doi:10.1016/j.molcel.2022.09.016)
+    - name: coactivator
+      dtype: string
+      description: Coactivator classification based on TFIID and/or SAGA dependence from Donczew et al., 2020 (doi:10.7554/eLife.50109)
+    - name: LCID_center
+      dtype: string
+      description: Genes near boundaries of chromosomal interacting domains from Swygert et al., 2020 (doi:10.1016/j.molcel.2018.11.020)
+    - name: Rossi_classes
+      dtype: string
+      description: Promoter classes from Rossi et al., 2021 (doi:10.1038/s41586-021-03314-8)
+    - name: RP_category
+      dtype: string
+      description: Ribosomal protein (RP) and ribosomal biogenesis (RiBi) gene classification from Zencir et al., 2020 (doi:10.1093/NAR/GKAA852)
+    - name: binding_cluster
+      dtype: string
+      description: Clusters from unsupervised K-means clustering using binary binding data of 178 transcription factors
+    - name: list_of_TFS_bound
+      dtype: string
+      description: List of transcription factors bound to gene promoter (-400 to +200 bp from TSS; Homer peak calling)
+    - name: number_of_bound_tfs
+      dtype: int64
+      description: Number of transcription factors bound to each promoter
+    - name: locus_tag
+      dtype: string
+      description: Systematic gene identifier from yeast_genome_resources dataset
+    - name: symbol
+      dtype: string
+      description: Standard gene symbol from yeast_genome_resources dataset
+
+- config_name: chec_seq
+  description: ChEC-seq transcription factor binding data with peak scores
+  default: true
+  data_files:
+  - split: train
+    path: chec_mahendrawada_2025.parquet
+  dataset_info:
+    features:
+    - 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: peak_score
+      dtype: float64
+      description: ChEC signal around peak center (sum of ChEC signal from -150 to +150 bp from peak summit) normalized to Drosophila spike-in control
+
+- config_name: rna_seq
+  description: Nascent RNA-seq differential expression data following transcription factor depletion using 4TU metabolic labeling
+  data_files:
+  - split: train
+    path: rnaseq_mahendrawada_2025.parquet
+  dataset_info:
+    features:
+    - name: regulator_locus_tag
+      dtype: string
+      description: Systematic gene name (ORF identifier) of the depleted transcription factor
+    - name: regulator_symbol
+      dtype: string
+      description: Standard gene symbol of the depleted transcription factor
+    - name: target_locus_tag
+      dtype: string
+      description: Systematic gene name (ORF identifier) of the differentially expressed target gene
+    - name: target_symbol
+      dtype: string
+      description: Standard gene symbol of the differentially expressed target gene
+    - name: log2fc
+      dtype: float64
+      description: Log2 fold change (IAA/DMSO) for significantly affected genes (DESeq2, padj <0.1, FC >= 1.3)
+---
+
+# Mahendrawada 2025
+
+This data is taken from the Supplement of
+
+[Mahendrawada, L., Warfield, L., Donczew, R. et al. Low overlap of transcription factor DNA binding and regulatory targets. Nature 642, 796–804 (2025). https://doi.org/10.1038/s41586-025-08916-0](https://doi.org/10.1038/s41586-025-08916-0)
+
+Please note that all column descriptions, except for those containing "locus_tag" and "symbol", are copy/pasted directly from the supplement or
+methods section of this paper.
+
+## Dataset Details
+
+The chec-seq and rna-seq data are taken from Supplemental Table 3. The feature data is taken from Supplemental table 2.
+See `scripts/` for more details on the parsing.
+
+Please note that the `peak_score` in the chec-seq data is unclearly documented. The methods section describes the peak calling
+process (using HOMER with specific thresholds) and the normalization method (reads per position divided by total D. melanogaster reads × 10,000),
+but the peak_score description in the supplement describes about summing signal in a ±150 bp window around the peak center. Presumably this refers
+to the HOMER feature annotation step.
+
+## Data Structure
+
+This dataset provides the following three parquet files
+
+### ChEC-seq
+
+| Field                 | Description                                                                                                                                |
+|-----------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
+| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the transcription factor                                                                         |
+| `regulator_symbol`    | Standard gene symbol of the transcription factor                                                                                           |
+| `target_locus_tag`    | Systematic gene name (ORF identifier) of the target gene                                                                                  |
+| `target_symbol`       | Standard gene symbol of the target gene                                                                                                    |
+| `peak_score`          | ChEC signal around peak center (sum of ChEC signal from -150 to +150 bp from peak summit) normalized to Drosophila spike-in control     |
+
+### RNA-seq
+
+| Field                 | Description                                                                                                                                |
+|-----------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
+| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the depleted transcription factor                                                                |
+| `regulator_symbol`    | Standard gene symbol of the depleted transcription factor                                                                                 |
+| `target_locus_tag`    | Systematic gene name (ORF identifier) of the differentially expressed target gene                                                         |
+| `target_symbol`       | Standard gene symbol of the differentially expressed target gene                                                                           |
+| `log2fc`              | Log2 fold change (IAA/DMSO) for significantly affected genes (DESeq2, padj <0.1, FC >= 1.3)                                             |
+
+### Features
+
+| Field                    | Description                                                                                                                                |
+|--------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
+| `gene_id`                | Systematic gene name (ORF identifier) from SGD (https://yeastgenome.org/)                                                                |
+| `SGD_id`                 | Unique identifier for each gene from SGD (https://yeastgenome.org/)                                                                      |
+| `gene_name`              | Common name of each gene                                                                                                                   |
+| `chr`                    | Chromosome number corresponding to gene                                                                                                    |
+| `strand`                 | Strandedness of the gene (+ or -)                                                                                                         |
+| `start`                  | Start position of the ORF                                                                                                                  |
+| `end`                    | End position of the ORF                                                                                                                    |
+| `TSS`                    | Transcription start site based on Park et al., 2014 (doi:10.1093/nar/gkt1366)                                                           |
+| `TATA_category`          | TATA box classification from Donczew et al., 2020 using consensus TATAWAW (doi:10.7554/eLife.50109)                                     |
+| `expression`             | Average signal normalized to gene length from Donczew et al., 2020 (doi:10.7554/eLife.50109)                                           |
+| `+1 nucleosome`          | Position of +1 nucleosome from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                                     |
+| `-1 nucleosome`          | Position of -1 nucleosome from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                                     |
+| `NDR Center`             | Center of nucleosome depleted region from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                         |
+| `NDR Width`              | Width of nucleosome depletion region from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                         |
+| `tail-dependence`        | Tail classification based on Mediator tail dependence from Warfield L, Donczew R et al., 2022 (doi:10.1016/j.molcel.2022.09.016)      |
+| `coactivator`            | Coactivator classification based on TFIID and/or SAGA dependence from Donczew et al., 2020 (doi:10.7554/eLife.50109)                   |
+| `LCID_center`            | Genes near boundaries of chromosomal interacting domains from Swygert et al., 2020 (doi:10.1016/j.molcel.2018.11.020)                  |
+| `Rossi_classes`          | Promoter classes from Rossi et al., 2021 (doi:10.1038/s41586-021-03314-8)                                                               |
+| `RP_category`            | Ribosomal protein (RP) and ribosomal biogenesis (RiBi) gene classification from Zencir et al., 2020 (doi:10.1093/NAR/GKAA852)          |
+| `binding_cluster`        | Clusters from unsupervised K-means clustering using binary binding data of 178 transcription factors                                     |
+| `list_of_TFS_bound`      | List of transcription factors bound to gene promoter (-400 to +200 bp from TSS; Homer peak calling)                                     |
+| `number_of_bound_tfs`    | Number of transcription factors bound to each promoter                                                                                     |
+| `locus_tag`              | Systematic gene identifier from yeast_genome_resources dataset                                                                             |
+| `symbol`                 | Standard gene symbol from yeast_genome_resources dataset                                                                                   |
+
+## Usage
+
+## Usage
+
+There are three parquet files in this repo. This is a way of getting that information programmatically
+
+```python
+from huggingface_hub import ModelCard
+from pprint import pprint
+
+card = ModelCard.load("BrentLab/hughes_2006", 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)
+```
+
+With the result
+
+```raw
+{'knockout': 'knockout.parquet',
+ 'metadata': 'metadata.parquet',
+ 'overexpression': 'overexpression.parquet'}
+```
+
+I recommend using `huggingface_hub.snapshot_download` to pull the repository. After that, use your favorite
+method of interacting with `parquet` files (eg duckDB, but you could use dplyr in R or pandas, too).
+
+```python
+from huggingface_hub import snapshot_download
+import duckdb
+import os
+
+repo_id = "BrentLab/hughes_2006"
+
+# Download entire repo to local directory
+repo_path = snapshot_download(
+    repo_id=repo_id,
+    repo_type="dataset"
+)
+
+print(f"Repository downloaded to: {repo_path}")
+
+# Construct path to the knockout parquet file
+parquet_path = os.path.join(repo_path, "knockout.parquet")
+print(f"Parquet file at: {parquet_path}")
+
+# Connect to DuckDB and query the parquet file
+conn = duckdb.connect()
+
+query = """
+SELECT * 
+FROM read_parquet(?)
+WHERE regulator_symbol = 'CST6'
+"""
+
+result = conn.execute(query, [parquet_path]).fetchall()
+print(f"Found {len(result)} rows for YJR060W")
+```