ArticlePloS one2012
The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- IsoFrog: a reversible jump Markov Chain Monte Carlo feature selection-based method for predicting isoform functions.Bioinformatics (Oxford, England) · 2023Article
- HSDatabase-a database of highly similar duplicate genes from plants, animals, and algae.Database : the journal of biological databases and curation · 2022Article
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- An overview of online resources for intra-species detection of gene duplications.Frontiers in genetics · 2022Review
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- The molecular basis, genetic control and pleiotropic effects of local gene co-expression.Nature communications · 2021Article
- JEDI: circular RNA prediction based on junction encoders and deep interaction among splice sites.Bioinformatics (Oxford, England) · 2021Article
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- IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation.Bioinformatics (Oxford, England) · 2021Article
- FIREWORKS: a bottom-up approach to integrative coessentiality network analysis.Life science alliance · 2021Article
- HSDFinder: A BLAST-Based Strategy for Identifying Highly Similar Duplicated Genes in Eukaryotic Genomes.Frontiers in bioinformatics · 2021Article
- Cost-Effective Mapping of Genetic Interactions in Mammalian Cells.Frontiers in genetics · 2021Article
- Tissue-specific usage of transposable element-derived promoters in mouse development.Genome biology · 2020Article
- Systematic analysis of bypass suppression of essential genes.Molecular systems biology · 2020Article
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThere has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD) was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available.
conclusionsThe Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.
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