README.md

---
license: mit
language:
  - en
tags:
  - genomics
  - yeast
  - transcription
  - binding
pretty_name: "Harbison, 2004 ChIP-chip"
size_categories:
  - 1M<n<10M
strain_information:
  background: W303
  base_strain: Z1256
# note: inferring from the heat shock condition, which is the only
# condition that explicitly mentions heat, the standard growth temperature
# is 30C
experimental_conditions:
  temperature_celsius: 30
doi: https://doi.org/10.1038/nature02800
citation: Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature.
configs:
- config_name: harbison_2004
  description: >-
    ChIP-chip data, primarily in standard YPD batch culture, but selected TFs were also tested in specific conditions where they were expected to be active.
  dataset_type: annotated_features
  default: true
  metadata_fields: ["regulator_locus_tag", "regulator_symbol", "condition"]
  data_files:
  - split: train
    path: harbison_2004.parquet
  dataset_info:
    features:
    - name: condition
      dtype:
        class_label:
          names: ["YPD", "SM", "RAPA", "H2O2Hi", "H2O2Lo",
                  "Acid", "Alpha", "BUT14", "BUT90", "Thi-",
                  "GAL", "HEAT", "Pi-", "RAFF"]
      description: >-
        Environmental condition of the experiment. Nearly all of the 204 regulators
        have a YPD condition, and some have others in addition.
      role: experimental_condition
      definitions:
        YPD:
          description: Standard YPD rich medium; the baseline condition for nearly all 204 regulators.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.8
            od600: 0.8
          media:
            # Harbison et al 2004: 1% yeast extract / 2% peptone / 2% glucose
            name: YPD
            carbon_source:
              - compound: D-glucose
                concentration_percent: 2
            nitrogen_source:
              - compound: yeast_extract
                concentration_percent: 1
              - compound: peptone
                concentration_percent: 2
        SM:
          description: Amino acid starvation induced by sulfometuron methyl (SM).
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.6
            od600: 0.6
          media:
            # Harbison et al 2004: synthetic complete medium
            name: synthetic_complete
          chemical_treatment:
            compound: sulfometuron_methyl
            # Harbison et al 2004: 0.2 mg/ml
            concentration_percent: 0.02
            duration_hours: 2
        RAPA:
          description: Rapamycin treatment in YPD to inhibit TORC1 signaling.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.8
            od600: 0.8
          media:
            name: YPD
            carbon_source:
              - compound: D-glucose
                concentration_percent: 2
            nitrogen_source:
              - compound: yeast_extract
                concentration_percent: 1
              - compound: peptone
                concentration_percent: 2
          chemical_treatment:
            compound: rapamycin
            # Harbison et al 2004: 100 nM
            concentration_percent: 9.142e-6
            duration_minutes: 20
        H2O2Hi:
          description: High-dose hydrogen peroxide (4 mM) oxidative stress treatment.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.5
            od600: 0.5
          media:
            name: YPD
            carbon_source:
              - compound: D-glucose
                concentration_percent: 2
            nitrogen_source:
              - compound: yeast_extract
                concentration_percent: 1
              - compound: peptone
                concentration_percent: 2
          chemical_treatment:
            compound: hydrogen_peroxide
            # Harbison et al 2004: 4 mM
            concentration_percent: 0.0136
            duration_minutes: 30
        H2O2Lo:
          description: Moderate-dose hydrogen peroxide (0.4 mM) oxidative stress treatment.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.5
            od600: 0.5
          media:
            name: YPD
            carbon_source:
              - compound: D-glucose
                concentration_percent: 2
            nitrogen_source:
              - compound: yeast_extract
                concentration_percent: 1
              - compound: peptone
                concentration_percent: 2
          chemical_treatment:
            compound: hydrogen_peroxide
            # Harbison et al 2004: 0.4 mM
            concentration_percent: 0.00136
            duration_minutes: 20
        Acid:
          description: Succinic acid treatment in YPD to reach pH 4.0.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.5
            od600: 0.5
          media:
            name: YPD
            carbon_source:
              - compound: D-glucose
                concentration_percent: 2
            nitrogen_source:
              - compound: yeast_extract
                concentration_percent: 1
              - compound: peptone
                concentration_percent: 2
          chemical_treatment:
            compound: succinic_acid
            # Harbison et al 2004: 0.05 M to reach pH 4.0
            concentration_percent: 0.59
            target_pH: 4.0
            duration_minutes: 30
        Alpha:
          description: Alpha-factor pheromone treatment to induce the mating response.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.8
            od600: 0.8
          media:
            name: YPD
            carbon_source:
              - compound: D-glucose
                concentration_percent: 2
            nitrogen_source:
              - compound: yeast_extract
                concentration_percent: 1
              - compound: peptone
                concentration_percent: 2
          chemical_treatment:
            compound: alpha_factor_pheromone
            # Harbison et al 2004: 5 mg/ml
            concentration_percent: 0.5
            duration_minutes: 30
        BUT14:
          description: YPD with 1% butanol for 14 hours to induce filamentous growth.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.8
            od600: 0.8
          media:
            # Harbison et al 2004: YPD containing 1% butanol
            name: YPD
            carbon_source:
              - compound: D-glucose
                concentration_percent: 2
            nitrogen_source:
              - compound: yeast_extract
                concentration_percent: 1
              - compound: peptone
                concentration_percent: 2
            additives:
              - compound: butanol
                concentration_percent: 1
          incubation_duration_hours: 14
        BUT90:
          description: YPD with 1% butanol for 90 minutes to induce filamentous growth.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.8
            od600: 0.8
          media:
            # Harbison et al 2004: YPD containing 1% butanol
            name: YPD
            carbon_source:
              - compound: D-glucose
                concentration_percent: 2
            nitrogen_source:
              - compound: yeast_extract
                concentration_percent: 1
              - compound: peptone
                concentration_percent: 2
            additives:
              - compound: butanol
                concentration_percent: 1
          incubation_duration_minutes: 90
        "Thi-":
          description: Synthetic complete medium lacking thiamine (vitamin B1).
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.8
            od600: 0.8
          media:
            # Harbison et al 2004: synthetic complete medium lacking thiamin
            name: synthetic_complete
        GAL:
          description: Galactose as sole carbon source in YEP medium.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.8
            od600: 0.8
          media:
            # Harbison et al 2004: YEP medium supplemented with galactose (2%)
            name: yeast_extract_peptone_galactose
            carbon_source:
              - compound: D-galactose
                concentration_percent: 2
        HEAT:
          description: Temperature shift from 30°C to 37°C for 45 minutes.
          # Harbison et al 2004: grown at 30°C, shifted to 37°C for 45 min
          temperature_celsius: 37
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.5
            od600: 0.5
          media:
            # Harbison et al 2004: YPD
            name: YPD
            carbon_source:
              - compound: D-glucose
                concentration_percent: 2
            nitrogen_source:
              - compound: yeast_extract
                concentration_percent: 1
              - compound: peptone
                concentration_percent: 2
        "Pi-":
          description: Synthetic complete medium lacking inorganic phosphate.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.8
            od600: 0.8
          media:
            # Harbison et al 2004: synthetic complete medium lacking phosphate
            name: synthetic_complete
        RAFF:
          description: Raffinose as sole carbon source in YEP medium.
          growth_phase_at_harvest:
            # Harbison et al 2004: OD600 ~0.8
            od600: 0.8
          media:
            # Harbison et al 2004: YEP medium supplemented with raffinose (2%)
            name: yeast_extract_peptone_raffinose
            carbon_source:
              - compound: D-raffinose
                concentration_percent: 2
    - name: regulator_locus_tag
      dtype: string
      description: Systematic gene name (ORF identifier) of the ChIPd transcription factor
      role: regulator_identifier
    - name: regulator_symbol
      dtype: string
      description: Standard gene symbol of the ChIPd transcription factor
      role: regulator_identifier
    - name: target_locus_tag
      dtype: string
      description: Systematic gene name (ORF identifier) of the target gene measured
      role: target_identifier
    - name: target_symbol
      dtype: string
      description: Standard gene symbol of the target gene measured
      role: target_identifier
    - name: effect
      dtype: float64
      description: The chip channel ratio (effect size)
      role: quantitative_measure
    - name: pvalue
      dtype: float64
      description: pvalue of the chip channel ratio (effect)
      role: quantitative_measure
---
# Harbison 2004

This Dataset is a parsed version of the data provided by Richard A. Young's lab at
[their website](http://younglab.wi.mit.edu/regulatory_code). DOI and citation are in
the dataset card above, or see the [ArrayExpress entry](https://www.ebi.ac.uk/biostudies/ArrayExpress/studies/E-WMIT-10?query=%22richard%20young%22)

## 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/harbison_2004")
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("harbison"))
vdb.query("SELECT * FROM harbison 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/harbison_2004",
    repo_type="dataset",
    allow_patterns="harbison_2004.parquet",
)
conn = duckdb.connect()
# returns a pandas DataFrame with the first 5 rows
conn.execute(
    "SELECT * FROM read_parquet(?) LIMIT 5",
    [f"{repo_path}/harbison_2004.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("harbison_2004.parquet")
```