ArticleGenome research2005
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
88 citing papers in PubMed, 1 synthesis or guideline pooled it, 177 citations in OpenAlex.
- Meta-analysis of expression signatures of muscle atrophy: gene interaction networks in early and late stages.BMC genomics · 2008Pooled it
- The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees.Genome biology · 2023Article
- Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation.Current opinion in genetics & development · 2020Review
- A comparison of gene expression and DNA methylation patterns across tissues and species.Genome research · 2020Article
- The essence of appetite: does olfactory receptor variation play a role?Journal of animal science · 2018Review
- Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral: (Nei Lecture, SMBE 2016, Gold Coast).Molecular biology and evolution · 2017Article
- Deep homology in the age of next-generation sequencing.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- Social regulation of the lymph node transcriptome in rhesus macaques (Macaca mulatta).Psychoneuroendocrinology · 2017Article
- Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri.BMC genomics · 2016Article
- A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics.eLife · 2015Article
- What to compare and how: Comparative transcriptomics for Evo-Devo.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2015Review
- Article
- Large-scale tag/PCR-based gene expression profiling.World journal of microbiology & biotechnology · 2014Review
- Genome-wide survey of interindividual differences of RNA stability in human lymphoblastoid cell lines.Scientific reports · 2013Article
- Evolutionary insights into scleractinian corals using comparative genomic hybridizations.BMC genomics · 2012Article
- Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio).BMC genomics · 2012Article
- The evolution of gene expression and the transcriptome-phenotype relationship.Seminars in cell & developmental biology · 2012Review
- Using genomic tools to study regulatory evolution.Methods in molecular biology (Clifton, N.J.) · 2012Review
- Expression divergence measured by transcriptome sequencing of four yeast species.BMC genomics · 2011Article
- Genetic mechanisms involved in the evolution of the cephalopod camera eye revealed by transcriptomic and developmental studies.BMC evolutionary biology · 2011Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Interspecies comparisons of gene expression levels will increase our understanding of the evolution of transcriptional mechanisms and help to identify targets of natural selection. This approach holds particular promise for apes, as many human-specific adaptations are thought to result from differences in gene expression rather than in coding sequence. To date, however, all studies directly comparing interspecies gene expression have been performed on single-species arrays, so that it has been impossible to distinguish differential hybridization due to sequence mismatches from underlying expression differences. To evaluate the severity of this potential problem, we constructed a new multiprimate cDNA array using probes from human, chimpanzee, orangutan, and rhesus. We find a large effect of sequence divergence on hybridization signal, even in the closest pair of species, human and chimpanzee. By comparing single-species array analyses with results from multispecies arrays, we examine how estimates of differential gene expression are affected by sequence divergence. Our results indicate that naive use of single-species arrays in direct interspecies comparisons can yield spurious results.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.