CARMEN Computational assessment of the expression-modulating potential for noncoding variants
Introduction
Large-scale genome-wide association and expression quantitative trait loci studies have identified multiple noncoding variants associated with genetic diseases via affecting gene expression. However, pinpointing the causal variants effectively and efficiently is still elusive. Here, we developed CARMEN, a novel algorithm to identify functional noncoding expression-modulating variants. Multiple evaluations demonstrate that CARMEN shows superior performance over state-of-the-art tools, and is able to pinpoint potentially causal variants other than lead SNPs reported by association studies. Meanwhile, benefitting from extensive annotations generated, CARMEN provides mechanism hints on predicted expression-modulating variants, enabling effectively characterizing functional variants involved in gene expression and disease-related phenotypes. CARMEN is well scale with massive dataset and is available online as a Web server at http://carmen.gao-lab.org.
Publications
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Credits
- Fang-Yuan Shi shify@mail.cbi.pku.edu.cn InvestigatorDeveloper
Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, China
- Yu Wang wangy@mail.cbi.pku.edu.cn InvestigatorDeveloper
Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, China
- Ge Gao gaog@mail.cbi.pku.edu.cn InvestigatorDeveloper
Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, China
Community Ratings
Usability | Efficiency | Reliability | Rated By |
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Accession | BT007274 |
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Tool Type | Application |
Category | Variant effect prediction |
Platforms | Linux/Unix |
Technologies | Java, Python2, R |
User Interface | Webpage, Terminal Command Line |
Input Data | VCF |
Latest Release | 1.0.0 (October 10, 2021) |
Download Count | 1061 |
Country/Region | China |
Submitted By | Fang-Yuan Shi |