Welcome to NanoMiner

NanoMiner contains data on human samples (634 samples) exposed to nanoparticles. All the samples in the NanoMiner have been annotated, preprocessed and normalized using standard methods that ensure the quality of the data analyses and enable users to utilize the database systematically across the different experimental setups and platforms. Pre-computed analysis results are saved in the database to facilitate visualization and statistical analysis of the data. NanoMiner provides several options (see the workflow diagram below) to visualize the expression values of the genes as well as to detect differentially expressed genes under different treatments.

*Last update was performed on June 2014:

About June 2014 updates: 2 new sets (GSE45869, GSE51186) including 64 samples have been added to NanoMiner.

About March 2014 update: 5 new sets (GSE42066, GSE42067, GSE42068, GSE43515, GSE45322) including 184 samples have been added to NanoMiner. Correlation Expression analysis has also been added at NanoMiner, and POMO (Plot Omic-associations on Multiple Organisms) Visualization has been enabled for the Correlation Expression analysis result.

Figure is the POMO visualization of genes coexpressed with HMGB1 (correlation value larger than 0.7) in dataset GSE16727 at NanoMiner.

Please use the below-mentioned publication to refer our work:
Kong L, Tuomela S, Hahne L, Ahlfors H, Yli-Harja O, Fadeel B, Lahesmaa R, Autio R.
NanoMiner - Integrative Human Transcriptomics Data Resource for Nanoparticle Research. PLoS One. 2013 Jul 12;8(7):e68414.

NanoMiner workflow diagram

With NanoMiner it is possible to 1) search for expression profiles of one or several genes of interest, 2) search and plot gene expression profiles within datasets, 3) cluster the samples within the datasets, 4) search for differentially expressed genes across several datasets, 5) analyze enriched KEGG-pathways and GO classes for the detected genes and 6) search the expression values of the genes in datasets belonging to a specific KEGG pathway or gene ontology. Further, NanoMiner database is also a valuable collection of available microarray data which can be also used by bioinformaticians as a data repository for future analyses.

NanoMiner utilizes R packages GOstats(v2.24.0), amap(v0.8-7), KEGG.db(v2.8.0), org.Hs.eg.db(v2.8.0), limma(v3.14.4), gplots(v2.10.1) in data analysis and illustration.

The cell types and the particulate matters used in the datasets in NanoMiner:

Reference Cell types Particulate matter Samples
GSE16727 (Busch et al.2010) human keratinocytes cell line (HaCaT) WC nanoparticles, WC-Co nanoparticles 40
GSE16425 (Fujita et al.2009) human keratinocytes cell line (HaCaT) ultrafine TiO2(T-7), fine TiO2(T-20), submicron TiO2(T-200) 36
GSE12405 (Gras et al.2009) human primary macrophages carboxilane dendrimer 2G-NN16 6
GSE8608 (Hofer et al.2008) monocyte-derived macrophages (MDM) from chronic obstructive pulmonary disease (COPD) patients and healthy subjects fine TiO2 and ultrafine Printex90 6
GSE7010 (Huang et al.2011) human primary epithelial cells coarse PM (Chapel Hill), fine PM (Chapel Hill), ultrafine PM (Chapel Hill) 12
GSE4567 (Karoly et al.2007) human primary pulmonary artery endothelial cells (HPAEC) ultrafine particle (Chapel Hill) 8
GSE14452 (Kawata et al.2009) human hepatoma cell line (HepG2) silver nanoparticles, polysthylene nanoparticles 15
E-TABM-679 human lung epithelial cell line (A549) carbon black, multiwall carbon nanotubes, silica nano, silica micro, silica quartz 36
GSE20677 (Kim et al.2012) human embryonic kidney cell line (293T), human peripheral blood mononuclear cells (PBMC) Au-nanoparticle EGFP oligonucleotide complex 16
GSE39330 (Tuomela et al. submitted) human monocyte-derived macrophages (HMDM), human monocyte-derived dendritic cells (MDDC), human T cell leukemia-derived cell line (Jurkat) ZnO-1 (IBU-tec advanced materials AG), ZnO-2 (mandelic acid coated ZnO-1), ZnO-3 (mercaptopropyl-trimethoxysilane coated ZnO-1), ZnO-4 (methoxyl coated ZnO), ZnO-5 (diethylene glycol modified ZnO), ZnO-9 (folic acid modified ZnO) 71
GSE39316 (Tuomela et al. submitted) human monocyte-derived macrophages (HMDM), human monocyte-derived dendritic cells (MDDC), human T cell leukemia-derived cell line (Jurkat) ZnO-1 (IBU-tec advanced materials AG), TiO2 (Evonik Degussa, Aeroxide TiO2 p25) 90
GSE14910 (Moos et al.2011) human colon cancer cells: CaCo-2, RKO nanoZnO, nanoFe2O3, nanoSiO2, nanoTiO2, Al2O3, nano-carbon black, microZnO 32
GSE25167 (Moos et al.2011) human skin-derived cancer cells (HaCaT and SK Mel-28) ZnO, TiO2, ZnCl2, ZnO_Transwell 15
GSE20431 (Balakumaran et al.2010) human bone marrow stromal cells Gold nanoparticles, FePro 15
GSE33278 (Hanagata et al.2011) Lung epithelial cells A549 exposured vs. non-treated cells. Hybridization: 2 replicates. Scanning: 3 replicates CuO nanoparticles 6

This database was part of the European Union FP7 research Nanommune project.

Start using NanoMiner from left hand side panel. For example, use 'Gene Search' to query for genes within sample sets and further to check their gene expression profiles.

Last update was performed on June 2014.