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Updated: Jul 31, 2026
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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
Published on: May 31, 2011
REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray
Crispin Roven1, Harmen J Bussemaker
1Department of Biological Sciences, Columbia University, New York, NY, USA.
Nucleic Acids Research
|June 26, 2003
Summary
REDUCE is a novel motif-based regression method for analyzing microarray data. It identifies DNA sequence motifs correlating with gene expression levels, aiding in understanding transcriptional regulation.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Microarray analysis is crucial for understanding gene expression.
- Identifying regulatory elements that control gene expression is a key challenge.
Purpose of the Study:
- To introduce REDUCE, a motif-based regression method for microarray data analysis.
- To identify DNA sequence motifs associated with gene expression levels.
Main Methods:
- REDUCE utilizes genome-wide mRNA abundances and regulatory DNA sequences.
- Unbiased statistics identify oligonucleotide motifs correlating with mRNA levels.
- Regression analysis infers the activity of motif-associated transcriptional modules.
Main Results:
- The method successfully identifies motifs linked to gene expression.
- It provides insights into transcriptional module activity.
Conclusions:
- REDUCE offers a powerful approach for motif discovery in gene regulation.
- The method is currently applicable to yeast, worm, and fly, with potential for other organisms.
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02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...