A novel heterogeneous network-based method for drug response prediction in cancer cell lines

Scientific Reports
Fei ZhangAo Li

Abstract

An enduring challenge in personalized medicine lies in selecting a suitable drug for each individual patient. Here we concentrate on predicting drug responses based on a cohort of genomic, chemical structure, and target information. Therefore, a recently study such as GDSC has provided an unprecedented opportunity to infer the potential relationships between cell line and drug. While existing approach rely primarily on regression, classification or multiple kernel learning to predict drug responses. Synthetic approach indicates drug target and protein-protein interaction could have the potential to improve the prediction performance of drug response. In this study, we propose a novel heterogeneous network-based method, named as HNMDRP, to accurately predict cell line-drug associations through incorporating heterogeneity relationship among cell line, drug and target. Compared to previous study, HNMDRP can make good use of above heterogeneous information to predict drug responses. The validity of our method is verified not only by plotting the ROC curve, but also by predicting novel cell line-drug sensitive associations which have dependable literature evidences. This allows us possibly to suggest potential sensitive associations...Continue Reading

References

Apr 17, 1998·The New England Journal of Medicine·J G ElmoreS W Fletcher
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Mar 17, 2000·Science·J Drews
Jun 21, 2001·Journal of Chemical Information and Computer Sciences·D Bonchev
Jul 1, 1993·Current Biology : CB·J SkolnickA Rey
Aug 5, 2008·Nature Methods·Gareth ButlandAndrew Emili
Mar 25, 2009·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Evanthia GalanisJan C Buckner
Nov 4, 2010·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Mar 23, 2011·Journal of Computational Chemistry·Chun Wei Yap
Jun 10, 2011·Molecular Systems Biology·Assaf GottliebRoded Sharan
Jan 20, 2012·The New England Journal of Medicine·Reza MirnezamiAra Darzi
Feb 14, 2012·Pharmaceutical Statistics·J L Sebaugh
Apr 28, 2012·Molecular BioSystems·Xing ChenGui-Ying Yan
Dec 4, 2012·Nucleic Acids Research·Andrea FranceschiniLars J Jensen
Jun 2, 2014·Nature Biotechnology·James C CostelloGustavo Stolovitzky
Jul 22, 2014·Journal of Chemical Information and Modeling·Muhammad Ammad-ud-dinSamuel Kaski
Sep 11, 2014·Nature·Michael Eisenstein
Aug 19, 2015·Briefings in Bioinformatics·Xing ChenYongdong Zhang
Sep 30, 2015·PLoS Computational Biology·Naiqian ZhangX Shirley Liu
Nov 20, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiaoyi Xu, Minghui Wang
Jul 12, 2016·Cell·Francesco IorioMathew J Garnett
Jul 16, 2016·PLoS Computational Biology·Xing ChenGuiying Yan
Jan 10, 2017·Scientific Reports·Zachary StanfieldMehmet Koyutürk
Jan 24, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics· Chen Peng, Ao Li

❮ Previous
Next ❯

Citations

Mar 10, 2019·Bioinformatics·Ladislav RampášekAnna Goldenberg
Feb 15, 2020·Briefings in Bioinformatics·Ziaurrehman TanoliMarkus Vähä-Koskela
Jun 23, 2020·NPJ Precision Oncology·George AdamAnna Goldenberg
Feb 11, 2020·Frontiers in Genetics·Jie LiYadong Wang
Jan 14, 2020·Briefings in Bioinformatics·Jinyu Chen, Louxin Zhang
Oct 21, 2020·Scientific Reports·Cheng QianNicholas D Sidiropoulos
Aug 18, 2020·Methods : a Companion to Methods in Enzymology·Liang YuYunhong Zha
Jul 11, 2020·Current Topics in Medicinal Chemistry·Xian TanHui Sun
Jan 29, 2021·Evidence-based Complementary and Alternative Medicine : ECAM·Jinghui WangHuifeng Zhu
Feb 18, 2021·NPJ Precision Oncology·George AdamAnna Goldenberg
May 24, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Fangyoumin FengHong Li
Aug 4, 2021·Journal of Chemical Information and Modeling·Iljung Jin, Hojung Nam
Aug 12, 2021·Computational and Structural Biotechnology Journal·Raihan RafiqueJulhash U Kazi
Oct 17, 2019·Molecular Pharmaceutics·Matteo ManicaMaría Rodríguez Martínez
Oct 8, 2021·Briefings in Bioinformatics·Farzaneh FiroozbakhtBenno Schwikowski

❮ Previous
Next ❯

Software Mentioned

SVMDRP
HNMDRP
PaDEL

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.