webTWAS 2.0: update platform for identifying complex disease susceptibility genes through transcriptome-wide
Chen Cao1, Mengting Shao1, Jianhua Wang2
1Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics, Nanjing Medical University,101 Longmian Ave, Nanjing, Jiangsu 211166, China.
Nucleic Acids Research
|November 11, 2024
Summary
webTWAS 2.0 enhances gene discovery for complex diseases using transcriptome-wide association studies (TWAS). This updated platform simplifies TWAS analysis and integrates extensive genetic data for researchers.
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- Transcriptome-wide association study (TWAS) has become a powerful tool for identifying complex disease susceptibility genes.
- Recent advancements focus on understanding how single nucleotide polymorphisms (SNPs) regulate gene expression, incorporating fine-mapping techniques.
- The exponential growth of genome-wide association study (GWAS) summary statistics necessitates updated resources.
Purpose of the Study:
- To introduce webTWAS 2.0, an enhanced platform for identifying human complex disease susceptibility genes using TWAS.
- To provide an integrated online TWAS analysis tool for researchers.
- To update the webTWAS resource with expanded GWAS summary statistics and multiple TWAS methods.
Main Methods:
- Integration of 7247 GWAS summary statistics from 192 publications, covering 1588 complex diseases.
- Implementation of multiple TWAS algorithms including sTF-TWAS, 3'aTWAS, and GIFT.
- Development of an interactive visualization tool and a personalized online analysis tool for user-submitted GWAS data.
Main Results:
- webTWAS 2.0 incorporates a significantly larger dataset of GWAS summary statistics and diverse TWAS methodologies.
- The platform offers an updated interactive visualization tool for exploring significant genetic associations.
- A refined search function and personalized analysis tool enhance user efficiency and data exploration.
Conclusions:
- webTWAS 2.0 provides a comprehensive and user-friendly platform for TWAS, facilitating the identification of complex disease genes.
- The updated resource and analysis tools support researchers in leveraging large-scale genetic data for gene discovery.
- The platform's accessibility and enhanced features aim to meet the evolving needs of the research community.
Related Concept Videos
01:11Genome-wide Association Studies-GWAS
12.5K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
12.5K
01:05Single Nucleotide Polymorphisms-SNPs
14.1K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
14.1K
02:02Genomics
36.0K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.0K
01:28Human Genetics
535
Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
The complex relationship between genetics and psychology is observable through common biological components such...
535
01:05Cancer-Critical Genes II: Tumor Suppressor Genes
7.3K
Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
7.3K
02:46Genetic Screens
4.9K
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
4.9K