Related Experiment Video
Updated: Oct 1, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
Published on: May 31, 2011
Automatic annotation of genomic regulatory sequences by searching for composite clusters
O V Kel-Margoulis1, T G Ivanova, E Wingender
1BIOBASE GmbH, Halchtersche Strasse 33, 38304 Wolfenbuettel, Germany.
Abstract:
A new method was developed for revealing of composite clusters of cis-elements in promoters of eukaryotic genes that are functionally related or coexpressed. A software system "ClusterScan" have been created that enables: (i) to train system on representative samples of promoters to reveal cis-elements that tend to cluster, (ii) to train system on a number of samples of functionally related promoters to identify functionally coupled transcription factors; (iii) to provide tools for searching of this clusters in genomic sequences to identify and functionally characterize regulatory regions in genome. A number of training samples of different functional and structural groups of promoters were analysed. Search for composite clusters in human chromosomes 21 and 22 reveals a number of interesting examples. Finally, a decision tree system was constructed to classify promoters of several functionally related gene groups. The decision tree system enables to identify new promoters and computationally predict their possible function.
More Related Videos
09:06High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
Published on: October 5, 2018
06:02A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
Published on: October 28, 2025
Related Concept Videos
Cis-regulatory Sequences
Cis-regulatory Sequences
Genome Annotation and Assembly
Cooperative Binding of Transcription Regulators
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Combinatorial Gene Control
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...