BrentLab/harbison_2004

Harbison 2004

This Dataset is a parsed version of the data provided by Richard A. Young's lab. To cite this data, please use:

Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99–104.doi:10.1038/nature02800

Dataset Details

The data was extract from The Young Lab's website.

I pulled the 'Excel' versions of both the P values (the downloaded file is called files_for_paper_abbr.zip) and Binding ratios (Ratio_forpaper_abbr.zip).

The following is copied from the Young's lab explanation of the analysis:

The microarrays were scanned using an Axon200B scanner, and the images were analyzed with Genepix 5.0. Columns corresponding to the background subtracted intensities and standard deviation of the background were extracted for further analysis. The intensities for the two channels, representing the immunoprecipitated (test) and unenriched (control) samples, were normalized by using the median of each channel to calculate a normalization factor, normalizing all datasets to a single median intensity. The log ratio of the intensity in the test channel to the control channel was calculated. To account for biases in the immunoprecipitation reaction, these log ratios were normalized for each spot by subtracting the average log ratio of each spot across all arrays. The intensities in the test channel were then adjusted to yield this normalized ratio. Finally, an error model was used to calculate significance of enrichment on each chip and to combine data for replicates to obtain a final average ratio and significance of enrichment for each intergenic region. Each intergenic region was assigned to the genes it is most likely to regulate. We have included new refinements in our analysis relative to that used in Lee et al. Notably, we have excluded artefactual spots from analysis, selected more reliable probes for normalization and assigned quality metrics to individual arrays to identify low quality experiments.

The script used to parse this data from the data provided by the Young lab into the parquet dataset presented here is included in scripts/

Dataset Structure

Field	Description
condition	See below for a definition of each level
regulator_locus_tag	The systematic ID of the ChIP'ed regulator.
regulator_symbol	The common name of the ChIP'ed regulator.
target_locus_tag	the systematic ID of the feature to which the Young lab assigned the effect/pvalue
target_symbol	the common name of the feature to which the Young lab assigned the effect/pvalue
effect	chip based binding ratio
pvalue	pvalue of the effect

• YPD: Rich media - Cells were grown in YPD (1% yeast extract/2% peptone/2% glucose) to an OD600 of ~0.8
• SM: Amino acid starvation - Cells were grown to an OD600 of ~0.6 in synthetic complete medium followed by treatment with the inhibitor of amino acid biosynthesis sulfometuron methyl (0.2 mg/ml final) for two hours
• RAPA: Nutrient deprived - Cells were grown in YPD to an OD600 of ~0.8 followed by treatment with rapamycin (100 nM final) for 20 minutes
• H2O2Hi: Highly hyperoxic - Cells were grown in YPD to an OD600 of ~0.5 followed by treatment with hydrogen peroxide (4 mM final) for 30 minutes
• H2O2Lo: Moderately hyperoxic - Cells were grown in YPD to an OD600 of ~0.5 followed by treatment with hydrogen peroxide (0.4 mM final) for 20 minutes
• Acid: Acidic medium - Cells were grown in YPD to an OD600 of ~0.5 followed by treatment for 30 minutes with succinic acid (0.05 M final) to reach a pH of 4.0
• Alpha: Mating inducing - Cells were grown in YPD to an OD600 of ~0.8 followed by treatment with the alpha factor pheromone (5 mg/ml) for 30 minutes
• BUT14: Filamentation inducing (14 hours) - Cells were grown in YPD containing 1% butanol for 14 hours (corresponding to an OD600 of ~0.8)
• BUT90: Filamentation inducing (90 minutes) - Cells were grown in YPD containing 1% butanol for 90 minutes (corresponding to an OD600 of ~0.8)
• Thi-: Vitamin deprived medium - Cells were grown in synthetic complete medium lacking thiamin to a final OD of ~0.8
• GAL: Galactose medium - Cells were grown in YEP medium supplemented with galactose (2%) to an OD600 of ~0.8
• HEAT: Elevated temperature - Cells were grown in YPD at 30°C to an OD600 of ~0.5 followed by a temperature shift to 37°C for 45 minutes
• Pi-: Phosphate deprived medium - Cells were grown in synthetic complete medium lacking phosphate to a final OD of ~0.8
• RAFF: Raffinose medium - Cells were grown in YEP medium supplemented with raffinose (2%) to an OD600 of ~0.8

Dataset Author and Contact: Chase Mateusiak @cmatKhan