ArticleBiology direct2010
Measuring gene expression divergence: the distance to keep.
Article in Biology direct, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.Genome biology · 2026Article
- Gene function predicts divergence across molecular levels.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary Divergence of mTOR-mediated Transcriptional Regulation BetweenbioRxiv : the preprint server for biology · 2026Article
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- SampleExplorer: using language models to discover relevant transcriptome data.Bioinformatics (Oxford, England) · 2024Article
- Fixation of Expression Divergences by Natural Selection inInternational journal of molecular sciences · 2024Article
- Phenotype prediction in plants is improved by integrating large-scale transcriptomic datasets.NAR genomics and bioinformatics · 2024Article
- Phytochemical fingerprint revealing antibacterial and antioxidant activities of endemic banana cultivars in Southeast Asia.Heliyon · 2024Article
- Initiation of a ZAKα-dependent ribotoxic stress response by the innate immunity endoribonuclease RNase L.Cell reports · 2024Article
- Extensive intratumor regional epigenetic heterogeneity in clear cell renal cell carcinoma targets kidney enhancers and is associated with poor outcome.Clinical epigenetics · 2023Article
- Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice.Plant communications · 2023Article
- Immune Cell Networks Uncover Candidate Biomarkers of Melanoma Immunotherapy Response.Journal of personalized medicine · 2022Article
- Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish.Nature genetics · 2021Article
- Tissue- and stage-specific landscape of the mouse translatome.Nucleic acids research · 2021Article
- Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation.Nucleic acids research · 2017Article
- Integrated analysis of the Plasmodium species transcriptome.EBioMedicine · 2016Article
- Host gene constraints and genomic context impact the expression and evolution of human microRNAs.Nature communications · 2016Article
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2 authors.
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Abstract
backgroundGene expression divergence is a phenotypic trait reflecting evolution of gene regulation and characterizing dissimilarity between species and between cells and tissues within the same species. Several distance measures, such as Euclidean and correlation-based distances have been proposed for measuring expression divergence.
resultsWe show that different distance measures identify different trends in gene expression patterns. When comparing orthologous genes in eight rat and human tissues, the Euclidean distance identified genes uniformly expressed in all tissues near the expression background as genes with the most conserved expression pattern. In contrast, correlation-based distance and generalized-average distance identified genes with concerted changes among homologous tissues as those most conserved. On the other hand, correlation-based distance, Euclidean distance and generalized-average distance highlight quite well the relatively high similarity of gene expression patterns in homologous tissues between species, compared to non-homologous tissues within species.
conclusionsDifferent trends exist in the high-dimensional numeric data, and to highlight a particular trend an appropriate distance measure needs to be chosen. The choice of the distance measure for measuring expression divergence can be dictated by the expression patterns that are of interest in a particular study.
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