Background: In the human genome, the transcription factors (TFs) and transcription factor-binding sites (TFBSs) network has a great regulatory function in the biological pathways. Such crosstalk might be affected by the single-nucleotide polymorphisms (SNPs), which could create or disrupt a TFBS, leading to either a disease or a phenotypic defect. Many computational resources have been introduced to predict the TFs binding variations due to SNPs inside TFBSs, sTRAP being one of them.
Methods: A literature review was performed and the experimental data for 18 TFBSs located in 12 genes was provided. The sequences of TFBS motifs were extracted using two different strategies; in the size similar with synthetic target sites used in the experimental techniques, and with 60 bp upstream and downstream of the SNPs. The sTRAP (http://trap.molgen.mpg.de/cgi-bin/trap_two_seq_form.cgi) was applied to compute the binding affinity scores of their cognate TFs in the context of reference and mutant sequences of TFBSs. The alternative bioinformatics model used in this study was regulatory analysis of variation in enhancers (RAVEN; http://www.cisreg.ca/cgi-bin/RAVEN/a). The bioinformatics outputs of our study were compared with experimental data, electrophoretic mobility shift assay (EMSA).
Results: In 6 out of 18 TFBSs in the following genes COL1A1, Hb ḉᴪ, TF, FIX, MBL2, NOS2A, the outputs of sTRAP were inconsistent with the results of EMSA. Furthermore, no p value of the difference between the two scores of binding affinity under the wild and mutant conditions of TFBSs was presented. Nor, were any criteria for preference or selection of any of the measurements of different matrices used for the same analysis.
Conclusion: Our preliminary study indicated some paradoxical results between sTRAP and experimental data. However, to link the data of sTRAP to the biological functions, its optimization via experimental procedures with the integration of expanded data and applying several other bioinformatics tools might be required.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216802 | PMC |
| http://dx.doi.org/10.1002/mgg3.1219 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Multimodal multiview bilinear graph convolutional network for mild cognitive impairment diagnosis.
Biomed Phys Eng Express
January 2025
Shandong University of Traditional Chinese Medicine, Qingdao Academy of Chinese Medical Sciences, Jinan, Shandong, 250355, CHINA.
Mild cognitive impairment (MCI) is a significant predictor of the early progression of Alzheimer's disease, and it can be used as an important indicator of disease progression. However, many existing methods focus mainly on the image itself when processing brain imaging data, ignoring other non-imaging data (e.g.
View Article and Find Full Text PDFLearning the language of antibody hypervariability.
Proc Natl Acad Sci U S A
January 2025
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139.
Protein language models (PLMs) have demonstrated impressive success in modeling proteins. However, general-purpose "foundational" PLMs have limited performance in modeling antibodies due to the latter's hypervariable regions, which do not conform to the evolutionary conservation principles that such models rely on. In this study, we propose a transfer learning framework called Antibody Mutagenesis-Augmented Processing (AbMAP), which fine-tunes foundational models for antibody-sequence inputs by supervising on antibody structure and binding specificity examples.
View Article and Find Full Text PDFThe Impact of Health Insurance on Mortality.
Annu Rev Public Health
January 2025
2Ross School of Business, University of Michigan, Ann Arbor, Michigan, USA.
A 2008 review in the considered the question of whether health insurance improves health. The answer was a cautious yes because few studies provided convincing causal evidence. We revisit this question by focusing on a single outcome: mortality.
View Article and Find Full Text PDFVoices of Nanomedicine: Blueprint Guidelines for Collaboration in Addressing Global Unmet Medical Needs.
ACS Nano
January 2025
NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade NOVA de Lisboa, Lisbon 1169-056, Portugal.
The "" under this Perspective underline the importance of interdisciplinary collaboration and partnerships across several disciplines, such as medical science and technology, medicine, bioengineering, and computational approaches, in bridging the gap between research, manufacturing, and clinical applications. Effective communication is key to bridging team gaps, enhancing trust, and resolving conflicts, thereby fostering teamwork and individual growth toward shared goals. Drawing from the success of the COVID-19 vaccine development, we advocate the application of similar collaborative models in other complex health areas such as nanomedicine and biomedical engineering.
View Article and Find Full Text PDFMuscle relaxation enhances motor imagery capacity in people with anxiety: A randomized clinical trial.
PLoS One
January 2025
Department of Nursing and Physiotherapy, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Spain.
Background: Motor imagery is the mental representation of a movement without physical execution. When motor imagery is performed to enhance motor learning and performance, participants must reach a temporal congruence between the imagined and actual movement execution. Identifying factors that can influence this capacity could enhance the effectiveness of motor imagery programs.
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!