Prediction of in vitro and in vivo oestrogen receptor activity using hierarchical clustering

SAR and QSAR in Environmental Research
Todd M Martin

Abstract

In this study, hierarchical clustering classification models were developed to predict in vitro and in vivo oestrogen receptor (ER) activity. Classification models were developed for binding, agonist, and antagonist in vitro ER activity and for mouse in vivo uterotrophic ER binding. In vitro classification models yielded balanced accuracies ranging from 0.65 to 0.85 for the external prediction set. In vivo ER classification models yielded balanced accuracies ranging from 0.72 to 0.83. If used as additional biological descriptors for in vivo models, in vitro scores were found to increase the prediction accuracy of in vivo ER models. If in vitro activity was used directly as a surrogate for in vivo activity, the results were poor (balanced accuracy ranged from 0.49 to 0.72). Under-sampling negative compounds in the training set was found to increase the coverage (fraction of chemicals which can be predicted) and increase prediction sensitivity.

References

Feb 24, 2001·Journal of Chemical Information and Computer Sciences·L M ShiD M Sheehan
Sep 12, 2006·Toxicological Sciences : an Official Journal of the Society of Toxicology·David J DixRobert J Kavlock
Feb 13, 2007·Journal of Molecular Graphics & Modelling·Huanxiang LiuPaola Gramatica
Feb 16, 2008·Science·Francis S CollinsJohn R Bucher
Mar 4, 2008·SAR and QSAR in Environmental Research·A PanayeJ M Porcher
Oct 23, 2009·Chemical Research in Toxicology·Hao ZhuAlexander Tropsha
Jan 1, 2008·Toxicology Mechanisms and Methods·Todd M MartinDouglas M Young
Apr 22, 2010·Journal of Chemical Information and Modeling·Jiazhong Li, Paola Gramatica
Dec 2, 2010·SAR and QSAR in Environmental Research·J Li, P Gramatica
Mar 11, 2011·SAR and QSAR in Environmental Research·G E JensenJ R Niemela
Oct 12, 2012·Environmental Health Perspectives·Daniel M RotroffRichard S Judson
Jan 9, 2013·Journal of Chemical Information and Modeling·Danielle NewbyTaravat Ghafourian
Jul 31, 2013·Toxicological Sciences : an Official Journal of the Society of Toxicology·Jie ShenHuixiao Hong
Aug 22, 2013·Journal of Chemical Information and Modeling·Todd M MartinMace G Barron
Feb 15, 2014·Journal of Chemical Information and Modeling·Alexey V ZakharovMarc C Nicklaus
Oct 6, 2014·Ecotoxicology and Environmental Safety·Yingjie ChenYun Tang
Aug 15, 2015·Toxicological Sciences : an Official Journal of the Society of Toxicology·Richard S JudsonRussell S Thomas

❮ Previous
Next ❯

Citations

Sep 25, 2020·PLoS Computational Biology·Rajib MukherjeeEfstratios N Pistikopoulos
Jun 28, 2018·Journal of Chemical Information and Modeling·Domenico GadaletaEnrico Mombelli
Apr 18, 2017·Chemical Research in Toxicology·Hanwen DuWeihua Li
Feb 25, 2019·ACS Sustainable Chemistry & Engineering·Michael A GonzalezRajender S Varma

❮ Previous
Next ❯

Methods Mentioned

BETA
Assay

Software Mentioned

CERAPP
ToxCast
MultiCase
ANN
CP
CoMFA
ChEMBL
Leadscope
Toxicity Estimation Software Tool ( TEST )
HQSAR

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.