ArticlePLoS computational biology2008
Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 47 citations in OpenAlex.
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- A degeneration-reducing criterion for optimal digital mapping of genetic codes.Computational and structural biotechnology journal · 2019Article
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- Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species.Genome biology and evolution · 2017Article
- Functional Translational Readthrough: A Systems Biology Perspective.PLoS genetics · 2016Review
- Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome.Genome biology and evolution · 2015Article
- Coding sequence density estimation via topological pressure.Journal of mathematical biology · 2015Article
- Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes.Cell reports · 2014Article
- Recognition of Protein-coding Genes Based on Z-curve Algorithms.Current genomics · 2014Article
- A Brief Review: The Z-curve Theory and its Application in Genome Analysis.Current genomics · 2014Article
- Type I Interferon Regulates the Expression of Long Non-Coding RNAs.Frontiers in immunology · 2014Article
- A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development.BMC genomics · 2013Article
- Comparison of RefSeq protein-coding regions in human and vertebrate genomes.BMC genomics · 2013Article
- Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.Cell · 2013Article
- Long non-coding RNAs in haematological malignancies.International journal of molecular sciences · 2013Review
- CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.Nucleic acids research · 2013Article
- Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression.PLoS genetics · 2013Article
- Potential roles of microRNAs in regulating long intergenic noncoding RNAs.BMC medical genomics · 2013Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparative genomics of multiple related species is a powerful methodology for the discovery of functional genomic elements, and its power should increase with the number of species compared. Here, we use 12 Drosophila genomes to study the power of comparative genomics metrics to distinguish between protein-coding and non-coding regions. First, we study the relative power of different comparative metrics and their relationship to single-species metrics. We find that even relatively simple multi-species metrics robustly outperform advanced single-species metrics, especially for shorter exons (< or =240 nt), which are common in animal genomes. Moreover, the two capture largely independent features of protein-coding genes, with different sensitivity/specificity trade-offs, such that their combinations lead to even greater discriminatory power. In addition, we study how discovery power scales with the number and phylogenetic distance of the genomes compared. We find that species at a broad range of distances are comparably effective informants for pairwise comparative gene identification, but that these are surpassed by multi-species comparisons at similar evolutionary divergence. In particular, while pairwise discovery power plateaued at larger distances and never outperformed the most advanced single-species metrics, multi-species comparisons continued to benefit even from the most distant species with no apparent saturation. Last, we find that genes in functional categories typically considered fast-evolving can nonetheless be recovered at very high rates using comparative methods. Our results have implications for comparative genomics analyses in any species, including the human.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.