Use Chou's 5-steps rule to identify DNase I hypersensitive sites via dinucleotide property matrix and extreme gradient boosting

Molecular Genetics and Genomics : MGG
Shengli Zhang, Tian Xue

Abstract

DNase I hypersensitive sites (DHSs) are highly sensitive active chromatin regions to DNase I enzymes, which provide the basis for the study of gene transcriptional regulation mechanism and play an important role in the analysis of gene expression regulatory elements. The identification of DHSs has contributed to biomedical research and genome analysis. There are already southern blotting technology and high-throughput sequencing technology to identify DHSs, but these experimental methods are often time-consuming and expensive, thus, novel and powerful computational methods are needed to predict DHSs. It is understood that researchers in related fields have proposed many feasible methods for the identification of DNase I hypersensitive sites. However, the accuracy of these methods is not satisfactory, so it is necessary to use more effective methods to predict DHSs. Therefore, on the basis of previous studies, we design a novel predictor called iDHS-DXG. First of all, we choose three sequence-derived feature representation methods to extract features, including kmer, mismatch and the dinucleotide property matrix based on Moran coefficient. Truncated singular value decomposition is selected for reducing the dimensionality of the ...Continue Reading

References

Mar 1, 1992·Protein Science : a Publication of the Protein Society·C T Zhang, K C Chou
Jan 1, 1988·Annual Review of Biochemistry·D S Gross, W T Garrard
Jan 1, 1995·Critical Reviews in Biochemistry and Molecular Biology·K C Chou, C T Zhang
Jan 24, 2003·Nature·Gary Felsenfeld, Mark Groudine
Mar 21, 2003·Journal of Proteome Research·Kuo-Chen Chou, David W Elrod
Mar 3, 2004·Bioinformatics·Christina S LeslieWilliam Stafford Noble
Jun 18, 2005·Bioinformatics·William Stafford NobleJohn Stamatoyannopoulos
Jul 27, 2005·Journal of Theoretical Biology·Yu-Dong CaiKuo-Chen Chou
Aug 19, 2007·Analytical Biochemistry·Kuo-Chen Chou, Hong-Bin Shen
Nov 3, 2007·Analytical Biochemistry·Hong-Bin Shen, Kuo-Chen Chou
Dec 21, 2010·Journal of Theoretical Biology·Kuo-Chen Chou
Feb 22, 2013·Bioinformatics·Dong-Sheng CaoYi-Zeng Liang
Apr 16, 2014·Analytical Biochemistry·Wei ChenKuo-Chen Chou
Dec 7, 2014·Bioinformatics·Rita Silvério-MachadoMarcos A Dos Santos
Dec 31, 2014·Medicinal Chemistry·Kuo-Chen Chou
Jul 5, 2015·Journal of Theoretical Biology·Guoqing LiuLu Cai
Jan 23, 2016·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Jianhua JiaKuo-Chen Chou
May 30, 2017·Journal of Theoretical Biology·Shanxin ZhangLindong Yang
Oct 14, 2017·Bioinformatics·Jake LeverJonathan Wren
Mar 30, 2018·Molecular Genetics and Genomics : MGG·Shanxin ZhangZhenghong Xu
Aug 14, 2018·Frontiers in Immunology·Balachandran ManavalanGwang Lee

❮ Previous
Next ❯

Citations

Mar 19, 2021·SAR and QSAR in Environmental Research·Y YaoY Liang

❮ Previous
Next ❯

Methods Mentioned

BETA
DNA-seq
feature extraction
XGBT

Software Mentioned

XGBoost
SVM
XGBT
Pse
SMOTE
RevcKmer
in
EL
DSET
DHSpred

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.