ArticleNucleic acids research2008
Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 2 of them syntheses that pooled it.
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Who cites it
46 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Identification of Aberrant Chromosomal Regions in Human Breast Cancer Using Gene Expression Data and Related Gene Information.Medical science monitor : international medical journal of experimental and clinical research · 2015Pooled it
- The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data.Blood · 2009Trial
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- LncMIR181A1HG is a novel chromatin-bound epigenetic suppressor of early stage osteogenic lineage commitment.Scientific reports · 2022Article
- Characterization of transcriptome diversity and in vitro behavior of primary human high-risk breast cells.Scientific reports · 2022Article
- Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci.Molecular biology and evolution · 2022Article
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- Muscle Proteomic and Transcriptomic Profiling of Healthy Aging and Metabolic Syndrome in Men.International journal of molecular sciences · 2021Article
- The impact of sex on gene expression across human tissues.Science (New York, N.Y.) · 2020Article
- Comparative analysis of metabolic and transcriptomic features ofJournal of the Royal Society, Interface · 2020Article
- Single-Gene Deletions Contributing to Loss of Heterozygosity inG3 (Bethesda, Md.) · 2019Article
- Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana.Planta · 2019Article
- Altered X-chromosome inactivation in T cells may promote sex-biased autoimmune diseases.JCI insight · 2019Article
- Chromosome-based gene co-expression analysis reveals regions associated with cancers: chromosome 1 as an example.Molecular biology reports · 2019Article
- Telomere length and telomerase activity in T cells are biomarkers of high-performing centenarians.Aging cell · 2019Article
- The expression of long noncoding RNA NEAT1 is reduced in schizophrenia and modulates oligodendrocytes transcription.NPJ schizophrenia · 2019Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The search for feature enrichment is a widely used method to characterize a set of genes. While several tools have been designed for nominal features such as Gene Ontology annotations or KEGG Pathways, very little has been proposed to tackle numerical features such as the chromosomal positions of genes. For instance, microarray studies typically generate gene lists that are differentially expressed in the sample subgroups under investigation, and when studying diseases caused by genome alterations, it is of great interest to delineate the chromosomal regions that are significantly enriched in these lists. In this article, we present a positional gene enrichment analysis method (PGE) for the identification of chromosomal regions that are significantly enriched in a given set of genes. The strength of our method relies on an original query optimization approach that allows to virtually consider all the possible chromosomal regions for enrichment, and on the multiple testing correction which discriminates truly enriched regions versus those that can occur by chance. We have developed a Web tool implementing this method applied to the human genome (http://www.esat.kuleuven.be/~bioiuser/pge). We validated PGE on published lists of differentially expressed genes. These analyses showed significant overrepresentation of known aberrant chromosomal regions.
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