Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

Beilstein Journal of Nanotechnology
Andrew Williams, Sabina Halappanavar

Abstract

The presence of diverse types of nanomaterials (NMs) in commerce is growing at an exponential pace. As a result, human exposure to these materials in the environment is inevitable, necessitating the need for rapid and reliable toxicity testing methods to accurately assess the potential hazards associated with NMs. In this study, we applied biclustering and gene set enrichment analysis methods to derive essential features of altered lung transcriptome following exposure to NMs that are associated with lung-specific diseases. Several datasets from public microarray repositories describing pulmonary diseases in mouse models following exposure to a variety of substances were examined and functionally related biclusters of genes showing similar expression profiles were identified. The identified biclusters were then used to conduct a gene set enrichment analysis on pulmonary gene expression profiles derived from mice exposed to nano-titanium dioxide (nano-TiO2), carbon black (CB) or carbon nanotubes (CNTs) to determine the disease significance of these data-driven gene sets. Biclusters representing inflammation (chemokine activity), DNA binding, cell cycle, apoptosis, reactive oxygen species (ROS) and fibrosis processes were identif...Continue Reading

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Citations

Dec 26, 2016·Toxicological Sciences : an Official Journal of the Society of Toxicology·Liecheng YangLeshuai W Zhang
Apr 21, 2018·Annals of the American Thoracic Society·Penny NymarkRoland C Grafström
Feb 18, 2016·Beilstein Journal of Nanotechnology·Rong Liu, Yoram Cohen
Jun 8, 2021·Frontiers in Public Health·Penny NymarkClemens Wittwehr

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Datasets Mentioned

BETA
GSE6858
GSE6116

Methods Mentioned

BETA
acetylation

Software Mentioned

affy
express
biclust
GSEA
R
Bimax
BioCyc
DAVID
LOWESS
MAPPFinder

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