+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Compound set enrichment: a novel approach to analysis of primary HTS data

Compound set enrichment: a novel approach to analysis of primary HTS data

Journal of Chemical Information and Modeling 50(12): 2067-2078

The main goal of high-throughput screening (HTS) is to identify active chemical series rather than just individual active compounds. In light of this goal, a new method (called compound set enrichment) to identify active chemical series from primary screening data is proposed. The method employs the scaffold tree compound classification in conjunction with the Kolmogorov-Smirnov statistic to assess the overall activity of a compound scaffold. The application of this method to seven PubChem data sets (containing between 9389 and 263679 molecules) is presented, and the ability of this method to identify compound classes with only weakly active compounds (potentially latent hits) is demonstrated. The analysis presented here shows how methods based on an activity cutoff can distort activity information, leading to the incorrect activity assignment of compound series. These results suggest that this method might have utility in the rational selection of active classes of compounds (and not just individual active compounds) for followup and validation.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 052269235

Download citation: RISBibTeXText

PMID: 21073183

DOI: 10.1021/ci100203e

Related references

Mining for bioactive scaffolds with scaffold networks: improved compound set enrichment from primary screening data. Journal of Chemical Information and Modeling 51(7): 1528-1538, 2011

Chemoinformatic analysis of NCI preclinical tumor data: evaluating compound efficacy from mouse xenograft data, NCI-60 screening data, and compound descriptors. Journal of Chemical Information and Modeling 47(4): 1414-1427, 2007

Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 18(4): 585-596, 2002

Knowledge Driven Variable Selection (KDVS) - a new approach to enrichment analysis of gene signatures obtained from high-throughput data. Source Code for Biology and Medicine 8(1): 2-2, 2013

Integrating machine learning techniques into robust data enrichment approach and its application to gene expression data. International Journal of Data Mining and Bioinformatics 8(3): 247-281, 2014

Quantitative approach to analysis of data from the Sigma kit for bloodspot newborn screening for galactose-1-phosphate uridyl transferase deficiency to detect compound heterozygotes with 25% net activity. Clinical Chemistry 48(6 Supplement): A29, June, 2002

Enrichment Disequilibrium: a novel approach for measuring the degree of enrichment after gene enrichment test. Biochemical and Biophysical Research Communications 424(3): 563-567, 2012

Early repositioning through compound set enrichment analysis: a knowledge-recycling strategy. Future Medicinal Chemistry 6(5): 563-575, 2014

Mesoporous silicate MCM-48 as an enrichment medium for ambient volatile organic compound analysis. Journal of Chromatography. A 1217(36): 5643-5651, 2010

Does quinone or phenol enrichment of humic substances alter the primary compound from a non-algicidal to an algicidal preparation?. Chemosphere 87(11): 1193-1200, 2012

Parametric analysis of the biomechanical response of head subjected to the primary blast loading--a data mining approach. Computer Methods in Biomechanics and Biomedical Engineering 19(10): 1053-1059, 2015

Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds. Molecular Genetics and Genomics 291(6): 2065-2079, 2016

Enrichment of health care data by informational constructs an output oriented modeling approach. Van Bemmel, J H , M J Ball And O Wigertz (Ed ) Ifip (International Federation For Information Processing) World Conference Series on Medical Informatics, Vol 4 Medinfo 83, Parts 1 And 2; Proceedings Of The World Conference, Amsterdam, Netherlands, Aug 22-27, Lvi+624p (Part 1); Xxxviii+680 (Part 2) North-Holland Publishing Co : Amsterdam, Netherlands; New York, N Y , Usa (Dist in The Usa And Canada By Elsevier Science Publishing Co , Inc : New York, N Y , Usa) Illus P1210-1, 1983

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach. Bioinformatics 31(16): 2601-2606, 2016

A new approach to phosphoserine and phosphothreonine analysis in peptides and proteins: chemical modification, enrichment via solid-phase reversible binding, and analysis by mass spectrometry. Analytical and Bioanalytical Chemistry 376(3): 366-373, 2003