ArticleEnvironmental science and pollution research international2013
GPR-Analyzer: a simple tool for quantitative analysis of hierarchical multispecies microarrays.
Article in Environmental science and pollution research international, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Seasonal dynamics of freshwater pathogens as measured by microarray at Lake Sapanca, a drinking water source in the north-eastern part of Turkey.Environmental monitoring and assessment · 2017Article
- Evolution of the MIDTAL microarray: the adaption and testing of oligonucleotide 18S and 28S rDNA probes and evaluation of subsequent microarray generations with Prymnesium spp. cultures and field samples.Environmental science and pollution research international · 2015Article
- SaDA: From Sampling to Data Analysis-An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data.International journal of environmental research and public health · 2015Article
- Molecular tools for the selective detection of nine diatom species biomarkers of various water quality levels.International journal of environmental research and public health · 2015Article
- Detection of emerging and re-emerging pathogens in surface waters close to an urban area.International journal of environmental research and public health · 2015Article
- Molecular detection of a potentially toxic diatom species.International journal of environmental research and public health · 2015Article
- Seasonal dynamics of harmful algae in outer Oslofjorden monitored by microarray, qPCR, and microscopy.Environmental science and pollution research international · 2013Article
- Molecular probes and microarrays for the detection of toxic algae in the genera Dinophysis and Phalacroma (Dinophyta).Environmental science and pollution research international · 2013Article
- Molecular probes for the detection and identification of ichthyotoxic marine microalgae of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta).Environmental science and pollution research international · 2013Article
- Microarray testing for the presence of toxic algae monitoring programme in Galicia (NW Spain).Environmental science and pollution research international · 2013Article
- Strengths and weaknesses of microarray approaches to detect Pseudo-nitzschia species in the field.Environmental science and pollution research international · 2013Article
- An evaluation of the applicability of microarrays for monitoring toxic algae in Irish coastal waters.Environmental science and pollution research international · 2013Article
- Testing a Microarray to Detect and Monitor Toxic Microalgae in Arcachon Bay in France.Microarrays (Basel, Switzerland) · 2013Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Monitoring of marine microalgae is important to predict and manage harmful algae blooms. It currently relies mainly on light-microscopic identification and enumeration of algal cells, yet several molecular tools are currently being developed to complement traditional methods. MIcroarray Detection of Toxic ALgae (MIDTAL) is an FP7-funded EU project aiming to establish a hierarchical multispecies microarray as one of these tools. Prototype arrays are currently being tested with field samples, yet the analysis of the large quantities of data generated by these arrays presents a challenge as suitable analysis tools or protocols are scarce. This paper proposes a two-part protocol for the analysis of the MIDTAL and other hierarchical multispecies arrays: Signal-to-noise ratios can be used to determine the presence or absence of signals and to identify potential false-positives considering parallel and hierarchical probes. In addition, normalized total signal intensities are recommended for comparisons between microarrays and in order to relate signals for specific probes to cell concentrations using external calibration curves. Hybridization- and probe-specific detection limits can be calculated to help evaluate negative results. The suggested analyses were implemented in "GPR-Analyzer", a platform-independent and graphical user interface-based application, enabling non-specialist users to quickly and quantitatively analyze hierarchical multispecies microarrays. It is available online at http://folk.uio.no/edvardse/gpranalyzer .
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