Datasets:

BrentLab
/

hu_2007_reimand_2010

sample_id int32 1 269	regulator_locus_tag stringclasses 269 values	regulator_symbol stringclasses 269 values	target_locus_tag stringlengths 7 9	target_symbol stringlengths 2 10	effect float64 -5.84 7.62	pval float64 0 1	average_od_of_replicates float64 0.11 1.47	heat_shock bool 1 class	tetracycline_treatment bool 2 classes	lowest_pval bool 2 classes	responsive bool 2 classes
1	YAL051W	OAF1	YBL084C	CDC27	0.147371	0.764681	0.82	false	false	true	false
1	YAL051W	OAF1	YBL113C	YBL113C	-0.104038	0.821078	0.82	false	false	true	false
1	YAL051W	OAF1	YBR030W	RKM3	-0.051578	0.898628	0.82	false	false	true	false
1	YAL051W	OAF1	YBL086C	YBL086C	0.048773	0.908446	0.82	false	false	true	false
1	YAL051W	OAF1	YBR002C	RER2	0.015823	0.971622	0.82	false	false	true	false
1	YAL051W	OAF1	YBR032W	YBR032W	-0.136777	0.805234	0.82	false	false	true	false
1	YAL051W	OAF1	YBL088C	TEL1	-0.075958	0.822727	0.82	false	false	true	false
1	YAL051W	OAF1	YBR004C	GPI18	0.04897	0.908324	0.82	false	false	true	false
1	YAL051W	OAF1	YBR034C	HMT1	-0.00354	0.993417	0.82	false	false	true	false
1	YAL051W	OAF1	YBL090W	MRP21	-0.250642	0.24986	0.82	false	false	true	false
1	YAL051W	OAF1	YBR006W	UGA2	0.113193	0.692471	0.82	false	false	true	false
1	YAL051W	OAF1	YBR036C	CSG2	-0.176025	0.605632	0.82	false	false	true	false
1	YAL051W	OAF1	YCL048W	SPS22	-0.027141	0.957619	0.82	false	false	true	false
1	YAL051W	OAF1	YCR010C	ADY2	-0.228091	0.383632	0.82	false	false	true	false
1	YAL051W	OAF1	YCR038C	BUD5	-0.044337	0.884349	0.82	false	false	true	false
1	YAL051W	OAF1	YCL050C	APA1	-0.10664	0.66222	0.82	false	false	true	false
1	YAL051W	OAF1	YCR012W	PGK1	0.025649	0.967688	0.82	false	false	true	false
1	YAL051W	OAF1	YCR040W	MATALPHA1	0.259185	0.163753	0.82	false	false	true	false
1	YAL051W	OAF1	YCL052C	PBN1	-0.145026	0.505932	0.82	false	false	true	false
1	YAL051W	OAF1	YCR014C	POL4	0.00669	0.986767	0.82	false	false	true	false
1	YAL051W	OAF1	YCR042C	TAF2	0.309792	0.203371	0.82	false	false	true	false
1	YAL051W	OAF1	YCL055W	KAR4	-0.103861	0.746333	0.82	false	false	true	false
1	YAL051W	OAF1	YCR016W	YCR016W	-0.142046	0.679129	0.82	false	false	true	false
1	YAL051W	OAF1	YCR044C	PER1	0.032211	0.938471	0.82	false	false	true	false
1	YAL051W	OAF1	YDR004W	RAD57	-0.097984	0.628084	0.82	false	false	true	false
1	YAL051W	OAF1	YDR034C-C	YDR034C-C	0.248066	0.505672	0.82	false	false	true	false
1	YAL051W	OAF1	YDR064W	RPS13	0.116847	0.769451	0.82	false	false	true	false
1	YAL051W	OAF1	YDR006C	SOK1	-0.070585	0.802654	0.82	false	false	true	false
1	YAL051W	OAF1	YDR034W-B	YDR034W-B	-0.12372	0.745164	0.82	false	false	true	false
1	YAL051W	OAF1	YDR066C	RTR2	-0.035446	0.910745	0.82	false	false	true	false
1	YAL051W	OAF1	YDR008C	YDR008C	-0.263564	0.314164	0.82	false	false	true	false
1	YAL051W	OAF1	YDR036C	EHD3	-0.047399	0.920721	0.82	false	false	true	false
1	YAL051W	OAF1	YDR068W	DOS2	-0.034058	0.954502	0.82	false	false	true	false
1	YAL051W	OAF1	YDR010C	YDR010C	-0.142908	0.651045	0.82	false	false	true	false
1	YAL051W	OAF1	YDR038C	ENA5	0.10114	0.727655	0.82	false	false	true	false
1	YAL051W	OAF1	YDR070C	FMP16	-0.209112	0.438904	0.82	false	false	true	false
1	YAL051W	OAF1	YDR366C	MOR1	0.177405	0.665723	0.82	false	false	true	false
1	YAL051W	OAF1	YDR398W	UTP5	-0.054943	0.863092	0.82	false	false	true	false
1	YAL051W	OAF1	YDR430C	CYM1	0.011849	0.981308	0.82	false	false	true	false
1	YAL051W	OAF1	YDR368W	YPR1	-0.021363	0.922387	0.82	false	false	true	false
1	YAL051W	OAF1	YDR400W	URH1	0.18926	0.46031	0.82	false	false	true	false
1	YAL051W	OAF1	YDR432W	NPL3	0.00752	0.987807	0.82	false	false	true	false
1	YAL051W	OAF1	YDR370C	DXO1	-0.313185	0.073759	0.82	false	false	true	false
1	YAL051W	OAF1	YDR402C	DIT2	-0.017208	0.974867	0.82	false	false	true	false
1	YAL051W	OAF1	YDR434W	GPI17	-0.007513	0.984036	0.82	false	false	true	false
1	YAL051W	OAF1	YDR372C	VPS74	-0.304579	0.107886	0.82	false	false	true	false
1	YAL051W	OAF1	YDR404C	RPB7	0.146118	0.519706	0.82	false	false	true	false
1	YAL051W	OAF1	YDR436W	PPZ2	0.00716	0.986863	0.82	false	false	true	false
1	YAL051W	OAF1	YER112W	LSM4	-0.180666	0.427517	0.82	false	false	true	false
1	YAL051W	OAF1	YER141W	COX15	-0.277178	0.14179	0.82	false	false	true	false
1	YAL051W	OAF1	YER172C	BRR2	0.084682	0.739889	0.82	false	false	true	false
1	YAL051W	OAF1	YER114C	BOI2	-0.358957	0.06613	0.82	false	false	true	false
1	YAL051W	OAF1	YER143W	DDI1	0.02785	0.924029	0.82	false	false	true	false
1	YAL051W	OAF1	YER174C	GRX4	-0.083906	0.794563	0.82	false	false	true	false
1	YAL051W	OAF1	YER116C	SLX8	-0.10576	0.714699	0.82	false	false	true	false
1	YAL051W	OAF1	YER145C	FTR1	0.205041	0.488122	0.82	false	false	true	false
1	YAL051W	OAF1	YER176W	ECM32	0.01612	0.967899	0.82	false	false	true	false
1	YAL051W	OAF1	YER118C	SHO1	0.01972	0.953488	0.82	false	false	true	false
1	YAL051W	OAF1	YER147C	SCC4	0.039191	0.896138	0.82	false	false	true	false
1	YAL051W	OAF1	YER178W	PDA1	-0.059243	0.843582	0.82	false	false	true	false
1	YAL051W	OAF1	YGL167C	PMR1	0.01676	0.956883	0.82	false	false	true	false
1	YAL051W	OAF1	YGL199C	YGL199C	-0.191387	0.381916	0.82	false	false	true	false
1	YAL051W	OAF1	YGL230C	YGL230C	0.214708	0.480462	0.82	false	false	true	false
1	YAL051W	OAF1	YGL169W	SUA5	0.139534	0.518086	0.82	false	false	true	false
1	YAL051W	OAF1	YGL201C	MCM6	-0.046348	0.884482	0.82	false	false	true	false
1	YAL051W	OAF1	YGL232W	TAN1	-0.182042	0.395003	0.82	false	false	true	false
1	YAL051W	OAF1	YGL171W	ROK1	-0.061885	0.874273	0.82	false	false	true	false
1	YAL051W	OAF1	YGL203C	KEX1	-0.198252	0.563518	0.82	false	false	true	false
1	YAL051W	OAF1	YGL234W	ADE57	-0.010937	0.986233	0.82	false	false	true	false
1	YAL051W	OAF1	YGL173C	XRN1	0.245327	0.233474	0.82	false	false	true	false
1	YAL051W	OAF1	YGL205W	POX1	-0.211875	0.6082	0.82	false	false	true	false
1	YAL051W	OAF1	YGL236C	MTO1	0.047806	0.901385	0.82	false	false	true	false
1	YAL051W	OAF1	YGR276C	RNH70	-0.204764	0.299599	0.82	false	false	true	false
1	YAL051W	OAF1	YHL010C	ETP1	-0.269723	0.311478	0.82	false	false	true	false
1	YAL051W	OAF1	YHL042W	YHL042W	-0.225057	0.378079	0.82	false	false	true	false
1	YAL051W	OAF1	YGR278W	CWC22	-0.419722	0.000099	0.82	false	false	true	true
1	YAL051W	OAF1	YHL012W	YHL012W	0.052812	0.86844	0.82	false	false	true	false
1	YAL051W	OAF1	YHL044W	YHL044W	-0.039179	0.916753	0.82	false	false	true	false
1	YAL051W	OAF1	YGR280C	PXR1	-0.158988	0.625698	0.82	false	false	true	false
1	YAL051W	OAF1	YHL014C	YLF2	-0.435137	0.003559	0.82	false	false	true	true
1	YAL051W	OAF1	YHL046C	PAU13	-0.118171	0.699657	0.82	false	false	true	false
1	YAL051W	OAF1	YGR282C	BGL2	0.011806	0.983928	0.82	false	false	true	false
1	YAL051W	OAF1	YHL016C	DUR3	0.237168	0.21865	0.82	false	false	true	false
1	YAL051W	OAF1	YHL048W	COS8	-0.081289	0.831779	0.82	false	false	true	false
1	YAL051W	OAF1	YIL078W	THS1	0.031638	0.956785	0.82	false	false	true	false
1	YAL051W	OAF1	YIL110W	HPM1	-0.104417	0.659522	0.82	false	false	true	false
1	YAL051W	OAF1	YIL142W	CCT2	-0.119472	0.629971	0.82	false	false	true	false
1	YAL051W	OAF1	YIL112W	HOS4	-0.031184	0.953834	0.82	false	false	true	false
1	YAL051W	OAF1	YIL144W	NDC80	-0.084981	0.825252	0.82	false	false	true	false
1	YAL051W	OAF1	YIL082W-A	YIL082W-A	-0.089183	0.832307	0.82	false	false	true	false
1	YAL051W	OAF1	YIL146C	ATG32	0.011928	0.977682	0.82	false	false	true	false
1	YAL051W	OAF1	YIL084C	SDS3	-0.03137	0.929855	0.82	false	false	true	false
1	YAL051W	OAF1	YIL116W	HIS5	-0.02332	0.954678	0.82	false	false	true	false
1	YAL051W	OAF1	YIL148W	RPL40A	-0.019862	0.97166	0.82	false	false	true	false
1	YAL051W	OAF1	YJR016C	ILV3	-0.135628	0.743871	0.82	false	false	true	false
1	YAL051W	OAF1	YJR048W	CYC1	-0.134159	0.592693	0.82	false	false	true	false
1	YAL051W	OAF1	YJR080C	AIM24	-0.161025	0.560087	0.82	false	false	true	false
1	YAL051W	OAF1	YJR018W	YJR018W	-0.035455	0.896083	0.82	false	false	true	false
1	YAL051W	OAF1	YJR050W	ISY1	0.073702	0.82748	0.82	false	false	true	false
1	YAL051W	OAF1	YJR083C	ACF4	-0.114399	0.715805	0.82	false	false	true	false

End of preview. Expand in Data Studio

Hu 2007 / Reimand 2010

Reimand et al reprocessed the Hu 2007 regulator knockout data set. This is a parsed version of that where the regulator and target features are harmonized with the BrentLab/yeast_genome_resources.

To cite this data, use:

Reimand J, Vaquerizas JM, Todd AE, Vilo J, Luscombe NM. Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. Nucleic Acids Res. 2010 Aug;38(14):4768-77. doi: 10.1093/nar/gkq232. Epub 2010 Apr 12. PMID: 20385592; PMCID: PMC2919724.

The original data was generated in the Iyer lab and published in:

Hu, Z., Killion, P. & Iyer, V. Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39, 683–687 (2007)

NOTE: the original paper does not describe the growth temperature

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/hu_2007_reimand_2010")
print([c.config_name for c in card.configs])  # list available datasets
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("hu_reimand"))
vdb.query("SELECT * FROM hu_reimand 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/hu_2007_reimand_2010",
    repo_type="dataset",
    allow_patterns="hu_2007_reimand_2010.parquet",
)
conn = duckdb.connect()
# returns a pandas DataFrame with the first 5 rows
conn.execute(
    "SELECT * FROM read_parquet(?) LIMIT 5",
    [f"{repo_path}/hu_2007_reimand_2010.parquet"],
).df()

Accessing using R

Clone the repository and read parquet files directly with arrow:

# install.packages("arrow")
arrow::read_parquet("hu_2007_reimand_2010.parquet")

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Collection including BrentLab/hu_2007_reimand_2010

yeastresources

Collection

Data collected and harmonized for the Brent lab at Washington University • 11 items • Updated Jan 7 • 1