Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data
One of the most important measures for detecting molecular adaptations between species/lineages at the gene level is the comparison of relative fixation rates of synonymous (dS) and non-synonymous (dN) mutations. This study shows that the branch model is sensitive to tree topology and proposes an al...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2013-01-01
|
| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.4137/EBO.S12166 |
| _version_ | 1828804992188809216 |
|---|---|
| author | Kyu-Won Kim David W. Burt Heebal Kim Seoae Cho |
| author_facet | Kyu-Won Kim David W. Burt Heebal Kim Seoae Cho |
| author_sort | Kyu-Won Kim |
| collection | DOAJ |
| description | One of the most important measures for detecting molecular adaptations between species/lineages at the gene level is the comparison of relative fixation rates of synonymous (dS) and non-synonymous (dN) mutations. This study shows that the branch model is sensitive to tree topology and proposes an alternative approach, devogs, which does not require phylogenetic topology for analysis. We compared devogs with a branch model method using virtual data and a varying ω ratio, in which parameters were obtained from real data. The positive predictive value, sensitivity, and specificity of the branch model were affected by the phylogenic tree topology. Devogs showed greater positive predictive value, whereas the branch model method had greater sensitivity. In a working example using devogs, a group of human RNA polymerase II-related genes, which are important in mediating alternative splicing, were significantly accelerated compared to four other mammals. |
| first_indexed | 2024-12-12T07:48:12Z |
| format | Article |
| id | doaj.art-eaaaab1990af4da3bd4001d0c38a4be5 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-12T07:48:12Z |
| publishDate | 2013-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-eaaaab1990af4da3bd4001d0c38a4be52022-12-22T00:32:31ZengSAGE PublishingEvolutionary Bioinformatics1176-93432013-01-01910.4137/EBO.S12166Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative DataKyu-Won Kim0David W. Burt1Heebal Kim2Seoae Cho3Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151–742, Korea.The Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh University, EH25 9RG, UK.Department of Agricultural Biotechnology, Seoul National University, Seoul 151–742, Korea.C&K genomics, 514 Main Building, Seoul National University Research Park, 1 Gwanak-ro, Gwanak-gu, Seoul 151–742, Korea.One of the most important measures for detecting molecular adaptations between species/lineages at the gene level is the comparison of relative fixation rates of synonymous (dS) and non-synonymous (dN) mutations. This study shows that the branch model is sensitive to tree topology and proposes an alternative approach, devogs, which does not require phylogenetic topology for analysis. We compared devogs with a branch model method using virtual data and a varying ω ratio, in which parameters were obtained from real data. The positive predictive value, sensitivity, and specificity of the branch model were affected by the phylogenic tree topology. Devogs showed greater positive predictive value, whereas the branch model method had greater sensitivity. In a working example using devogs, a group of human RNA polymerase II-related genes, which are important in mediating alternative splicing, were significantly accelerated compared to four other mammals.https://doi.org/10.4137/EBO.S12166 |
| spellingShingle | Kyu-Won Kim David W. Burt Heebal Kim Seoae Cho Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data Evolutionary Bioinformatics |
| title | Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data |
| title_full | Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data |
| title_fullStr | Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data |
| title_full_unstemmed | Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data |
| title_short | Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data |
| title_sort | identification of differentially evolved genes an alternative approach to detection of accelerated molecular evolution from genome wide comparative data |
| url | https://doi.org/10.4137/EBO.S12166 |
| work_keys_str_mv | AT kyuwonkim identificationofdifferentiallyevolvedgenesanalternativeapproachtodetectionofacceleratedmolecularevolutionfromgenomewidecomparativedata AT davidwburt identificationofdifferentiallyevolvedgenesanalternativeapproachtodetectionofacceleratedmolecularevolutionfromgenomewidecomparativedata AT heebalkim identificationofdifferentiallyevolvedgenesanalternativeapproachtodetectionofacceleratedmolecularevolutionfromgenomewidecomparativedata AT seoaecho identificationofdifferentiallyevolvedgenesanalternativeapproachtodetectionofacceleratedmolecularevolutionfromgenomewidecomparativedata |