On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery methods. We assign position-specific prior distributions to the frequency parameters of the model, penalizing deviations from a specified conservation profile. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC463320 | PMC |
| http://dx.doi.org/10.1186/gb-2004-5-7-r50 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.
Bioinformatics
January 2025
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium.
Summary: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly.
View Article and Find Full Text PDFMicroRNAs' Significance in Retinoblastoma Diagnosis and Treatment: The Little Heroes.
Biochem Genet
January 2025
Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
One in 16, 000 live births is affected by the retinal tumor RB (retinoblastoma), which is frequently found in a child's early years. Both of the RB1 alleles that have been locally mutated in the affected retina are present in 60 percent of cases. Retinoblastoma (RB) can be detected using a variety of techniques, including imaging of the brain and orbits, eye examinations under anesthesia (EUAs), and the discovery of cell-free tumor DNA in samples of aqueous humor or plasma.
View Article and Find Full Text PDFCRISPR-Cas12a-Mediated Growth of Gold Nanoparticles for DNA Detection in Agarose Gel.
ACS Sens
January 2025
Department of Clinical Laboratory of Sir Run Run Shaw Hospital, College of Biosystems Engineering and Food Science, Zhejiang University School of Medicine, Hangzhou 310058, People's Republic of China.
The rapid, simple, and sensitive detection of nucleic acid biomarkers plays a significant role in clinical diagnosis. Herein, we develop a label-free and point-of-care approach for isothermal DNA detection through the trans-cleavage activity of CRISPR-Cas12 and the growth of gold nanomaterials in agarose gel. The presence of the target can activate CRISPR-Cas12a to cleave single-stranded DNA, thus modulating the length and number of DNA sequences that mediate the growth of gold nanoparticles (AuNPs) or gold nanorods (AuNRs).
View Article and Find Full Text PDFIsoferulic Acid Inhibits Proliferation and Migration of Pancreatic Cancer Cells, and Promotes the Apoptosis of Pancreatic Cancer Cells in a Mitochondria-Dependent Manner Through Inhibiting NF-κB Signalling Pathway.
Clin Exp Pharmacol Physiol
March 2025
Department of Endocrinology, The Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, People's Republic of China.
Isoferulic acid (IA), a derivative of cinnamic acid, is derived from Danshen and exhibits anticancer properties by disrupting cancer cell activities. However, its role in pancreatic cancer, the "king of cancer", was unknown. In this study, pancreatic cancer cells were subjected to treatment with IA (6.
View Article and Find Full Text PDFBetacoronaviruses Differentially Activate the Integrated Stress Response to Optimize Viral Replication in Lung-Derived Cell Lines.
Viruses
January 2025
Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
The betacoronavirus genus contains five of the seven human coronaviruses, making it a particularly critical area of research to prepare for future viral emergence. We utilized three human betacoronaviruses, one from each subgenus-HCoV-OC43 (embecovirus), SARS-CoV-2 (sarbecovirus), and MERS-CoV (merbecovirus)-, to study betacoronavirus interactions with the PKR-like ER kinase (PERK) pathway of the integrated stress response (ISR)/unfolded protein response (UPR). The PERK pathway becomes activated by an abundance of unfolded proteins within the endoplasmic reticulum (ER), leading to phosphorylation of eIF2α and translational attenuation.
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!