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YCRD: Yeast Combinatorial Regulation Database.

Wei-Sheng Wu1, Yen-Chen Hsieh1, Fu-Jou Lai1

  • 1Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan.

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|July 9, 2016
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Summary
This summary is machine-generated.

A new database, the Yeast Combinatorial Regulation Database (YCRD), catalogs over 434,000 regulatory associations between cooperative transcription factor pairs and genes. This resource aids researchers in understanding gene expression control in yeast.

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Area of Science:

  • Molecular Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Transcriptional control in eukaryotes relies on cooperative transcription factors (TFs).
  • Existing public databases lack comprehensive data on cooperative TF regulatory associations.
  • Understanding these interactions is crucial for studying gene expression mechanisms.

Purpose of the Study:

  • To develop the Yeast Combinatorial Regulation Database (YCRD).
  • To provide a centralized resource for TF pair-gene regulatory associations in yeast.
  • To facilitate research into combinatorial gene regulation.

Main Methods:

  • Compiled data from 17 algorithms to identify over 2500 cooperative TF pairs.
  • Defined target genes as common targets of TF pairs, using data from the YEASTRACT database.
  • Integrated 434,197 regulatory associations between TF pairs and 6243 genes.

Main Results:

  • The YCRD contains 434,197 regulatory associations.
  • It includes 2535 cooperative TF pairs and 6243 genes.
  • The database allows searching for target genes, regulating TF pairs, and key TF pairs for specific gene sets.

Conclusions:

  • YCRD is a valuable resource for yeast biologists.
  • It supports the study of combinatorial regulation of gene expression.
  • The database enhances understanding of molecular mechanisms in transcriptional regulation.