A general and detailed noise model for the DNA microarray measurement of gene expression is presented and used to derive a Bayesian estimation scheme for expression ratios, implemented in a program called PFOLD, which provides not only an estimate of the fold-change in gene expression, but also confidence limits for the change and a P-value quantifying the significance of the change. Although the focus is on oligonucleotide microarray technologies, the scheme can also be applied to cDNA based technologies if parameters for the noise model are provided. The model unifies estimation for all signals in that it provides a seamless transition from very low to very high signal-to-noise ratios, an essential feature for current microarray technologies for which the median signal-to-noise ratios are always moderate. The dual use, as decision statistics in a two-dimensional space, of the P-value and the fold-change is shown to be effective in the ubiquitous problem of detecting changing genes against a background of unchanging genes, leading to markedly higher sensitivities, at equal selectivity, than detection and selection based on the fold-change alone, a current practice until now.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1089/106652701753307502 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
MAPK-CncC Signaling Pathways Regulate the Antitoxic Response to Avermectin-Induced Oxidative Stress in Juvenile Chinese Mitten Crab, .
Environ Sci Technol
January 2025
Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang 415000 Sichuan Province, China.
This study delves into the adverse effects of AVM, emphasizing oxidative stress induction in the Chinese mitten crab, , and the role of the MAPK-CncC signaling pathway in mediating the antioxidative response. Our findings reveal a dose-dependent impairment in growth performance, alongside occurrence of oxidative stress. The activity of CAT and superoxide dismutase increased significantly in all treatments (0.
View Article and Find Full Text PDFNatural variations in and its neighboring confer yellow seed with elevated oil content in .
Proc Natl Acad Sci U S A
February 2025
College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
Seed color is a critical quality trait in numerous plant species. In oilseed crops, including rapeseed and mustard, yellow seeds are distinguished by their significantly higher oil content and faster germination rates compared to black or brown counterparts. Despite the agronomic significance of the yellow seeds being a prime breeding target, the mechanisms underlying elevated oil content remain obscure.
View Article and Find Full Text PDFCBX2 suppresses interferon signaling to diminish tumor immunogenicity via a noncanonical corepressor complex.
Proc Natl Acad Sci U S A
February 2025
State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510050, China.
Chromobox 2 (CBX2), a crucial component of the polycomb repressive complex (PRC), has been implicated in the development of various human cancers. However, its role in the regulation of tumor immunogenicity and immune evasion remains inadequately understood. In this study, we found that ablation of CBX2 led to tumor growth inhibition, activation of the tumor immune microenvironment, and enhanced therapeutic efficacy of anti-PD1 or adoptive T cell therapies by using murine syngeneic tumor models.
View Article and Find Full Text PDFPlastic responses to past environments shape adaptation to novel selection pressures.
Proc Natl Acad Sci U S A
February 2025
Molecular Ecology and Evolution Group, School of Environmental and Natural Sciences, Bangor University, Bangor LL57 2UW, United Kingdom.
Phenotypic plasticity may pave the way for rapid adaptation to newly encountered environments. Although it is often contested, there is growing evidence that initial plastic responses of ancestral populations to new environmental cues may promote subsequent adaptation. However, we do not know whether plasticity to cues present in the ancestral habitat (past-cue plasticity) can facilitate adaptation to novel cues.
View Article and Find Full Text PDFWe lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into repetitive sequences, up to 1697 per cell line, which enables generating large-scale deletions, inversions, translocations, and circular DNA. Recombinase induction produced more than 100 stochastic megabase-sized rearrangements in each cell.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!