ReviewMethods in molecular biology (Clifton, N.J.)2009
Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.
Review in Methods in molecular biology (Clifton, N.J.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
7 citing papers in PubMed.
- Mathematical Modeling and Computational Prediction of High-Risk Types of Human Papillomaviruses.Computational and mathematical methods in medicine · 2022Article
- In silico analysis of high affinity potassium transporter (HKT) isoforms in different plants.Aquatic biosystems · 2014Article
- Bugs in the system.Immunological reviews · 2013Review
- Article
- Massive-scale gene co-expression network construction and robustness testing using random matrix theory.PloS one · 2013Article
- Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns.BMC bioinformatics · 2011Article
- The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks.Plant physiology · 2010Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Reliable identification and assignment of cis-regulatory elements in promoter regions is a challenging problem in biology. The sophistication of transcriptional regulation in higher eukaryotes, particularly in metazoans, could be an important factor contributing to their organismal complexity. Here we present an integrated approach where networks of co-expressed genes are combined with gene ontology-derived functional networks to discover clusters of genes that share both similar expression patterns and functions. Regulatory elements are identified in the promoter regions of these gene clusters using a Gibbs sampling algorithm implemented in the A-GLAM software package. Using this approach, we analyze the cell-cycle co-expression network of the yeast Saccharomyces cerevisiae, showing that this approach correctly identifies cis-regulatory elements present in clusters of co-expressed genes.
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Registered trials
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