Improved feature-based prediction of SNPs in human cytochrome P450 enzymes

Interdisciplinary Sciences, Computational Life Sciences
Li LiDong-Qing Wei

Abstract

Single nucleotide polymorphisms (SNPs) make up the most common form of mutations in human cytochrome P450 enzymes family, and have the potential to bring with different drug responses or specific diseases in individual patients. Here, based on machine learning technology, we aim to explore an effective set of sequence-based features for improving prediction of SNPs by using support vector machine algorithms. The features are derived from the target residues and flanking protein sequences, such as amino acid types, sequences composition, physicochemical properties, position-specific scoring matrix, phylogenetic entropy and the number of possible codons of target residues. In order to deal with the imbalance data with a majority of non-SNPs and a minority of SNPs, a preprocessing strategy based on fuzzy set theory was applied to the datasets. Our final model achieves the performance of 93.8% in sensitivity, 88.8% in specificity, 91.3% in accuracy and 0.971 of AUC value, which is significantly higher than the previous DNA sequence-based or protein sequence-based methods. Furthermore, our study also suggested the roles of individual features for prediction of SNPs. The most important features consist of the amino acid type, the num...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
May 10, 2000·Nature Biotechnology·J J McCarthy, R Hilfiker
May 5, 2001·Genome Research·P C Ng, S Henikoff
Aug 31, 2002·Nucleic Acids Research·Vasily RamenskyShamil Sunyaev
Feb 18, 2005·Nature Reviews. Genetics·Joel N Hirschhorn, Mark J Daly
Aug 25, 2007·Pharmacogenomics·Anton A Komar
Nov 1, 2008·Bioinformatics·Andrew D JohnsonPaul I W de Bakker
Feb 13, 2010·Journal of Cheminformatics·Amanda C Schierz
Mar 30, 2010·Computers in Biology and Medicine·Der-Chiang LiSusan C Hu
Apr 1, 2010·Nature Methods·Ivan A AdzhubeiShamil R Sunyaev
Sep 17, 2011·Protein and Peptide Letters·Li LiKuo-Chen Chou
Feb 1, 2012·Expert Opinion on Drug Metabolism & Toxicology·Joseph McGraw, Donald Waller
Mar 10, 2012·Molecular BioSystems·Shao-Ping ShiRu-Ping Liang
Apr 3, 2012·Bioinformatics·Erola PairóAlexandre Perera
Apr 14, 2012·Statistical Applications in Genetics and Molecular Biology·Malay BhattacharyyaSanghamitra Bandyopadhyay
May 18, 2012·Current Drug Metabolism·Li LiDong-Qing Wei
Jun 13, 2012·Nucleic Acids Research·Ngak-Leng SimPauline C Ng
Jun 6, 2013·Bioinformatics·Orion J BuskeMichael Brudno
Oct 16, 2014·Bioinformatics·Tune H PersJoel N Hirschhorn

❮ Previous
Next ❯

Citations

Feb 7, 2018·International Journal of Molecular Sciences·Li-Yue BaiDong-Qing Wei
Apr 5, 2018·Frontiers in Microbiology·Balachandran ManavalanGwang Lee
Jun 3, 2021·International Journal of Environmental Research and Public Health·Shu-Farn TeyWen-Shiann Wu

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.