Public microarray data

This section describes the use of the microarray technology for transcriptional profiling. The section includes a summary of the experimental procedures (section on Experimental design), the most widely used array platforms (section on Platforms for Gene Expression Analysis), and briefly summarizes the data analysis steps, the software that can be used, and the public microarray data repositories (sections on Analysis of microarray data and Data sharing). 

Persson S., Wei H., Milne X, Page G.D., P. and Somerville C. (2005). Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc. Natl. Acad. Sci. USA 102 8633-8638. 

Many algorithms have been used effectively with DNA microarray data for predicting of a binary outcome, e g., response versus non-response. Dudoit et al. (3) compared several algorithms using several publicly available data sets. A linear discriminant is a function... 

One of the most pressing concerns in the field is that the lack of correct data format and comparability of microarray experiments will limit future integrative microarray research and the ability of performing meta analysis of microarray data available in the public domain (39,40). 

It is one of eleven Programs for Genomic Applications (PGAs) funded by the National Heart, Lung and Blood Institute (NHLBI) of the NIH. The CardioGenomics PGA Public Data (http //cardiogenomics.med.harvard. edu/public-data.tcl) provides microarray data on a number of cardiac-related disease topics. 

The MIAME standard defines the minimum information investigators must report for a microarray experiment to be reproduced. The MAGE standard was born partially from MIAME, and the European Bioinformatics Institute used MIAME and MAGE to guide the development of ArrayEx-press, their public genomic data repository (34). Sample annotation lies at the heart of MIAME, underscoring the need to understand as completely as possible the experimental conditions that may influence the microarray data. Many journals that publish microarray data require the submission of MIAME-supportive microarray data to a public genomic data repository as a condition of publication. These typically include submission of protocols species, strains, and sex used for in vivo studies cell line name and culture conditions for in vitro studies, and other relevant information. 

Tong W, Harris S, Cao X, et al. Development of public toxicogenomics software for microarray data management and analysis. MutatRes. 2004 549(l-2) 241-253. 

A quick search in the PubMed database shows that the number of scientific publications in the microarray area grew exponentially since its introduction in 1995 and remained at 7000 in recent years. Despite its revolutionary growth in the research area, the microarray technique has been slow in penetration in the molecular diagnostic market, as it accounted for only 10% of the whole molecular diagnostic market in 2010 (7). The rather serious concerns about the reproducibility and robustness of microarray data, discussed previously, deterred receiving regulatory approval as well as obtaining success in... 

We focus on the combination of transcriptomics and metabolomics and more specifically on microarray data, which is currently the most used method for gene expression profiling and is used on a routine basis. In the first paragraphs, we briefly revise the extraction of mRNA or metabolites, their measurement, quality control of data, and analysis methods. Afterward two different types of data fusion and recent tools and publications are reviewed, followed by visualization methods for obtained data. Lastly, the metabolite annotation Web server MassTRIX is presented. This Web server allows combined analysis of transcriptomic and metabolomic data in the context of metabolic pathways. We compared the metabolomics part against similar tools and give a short outlook on the next version of MassTRIX, MassTRIX 4. 

Life Sciences Institute. URL http //www.mged.org/workgroups/ rsbi/MIAME-Tox checklist.doc. Guide for authors, journal editors and referees to help ensure that microarray data supporting published results are made publicly available in a format that enables rmambiguous interpretation of the data and potential verification of the conclusions. 

Although compliance with MGED guidelines is still somewhat limited, it is of note that journals such as Nature, Cell, and The Lancet have adopted these guidelines for submitting microarray expression data for publication. In addition to demanding MIAME-compliant data, Nature and Cell require authors to submit their microarray data to a public repository as a precondition... 

Figure 9.5 Illustration of genes expressed similarly during a time course of somatic cmbryogcnesis in one of the K-mcans cluster sets, set 6, of the microarray data. Adapted from Thibaud-Nissen, e( al The annotations matching clone IDs on the microarray sets represent the top Blastx hit in the public databases at a threshold of K -6. The putative function in cell metabolism is shown oth, other ox, oxidative strcss/dcfcnsc sig, signaling to, transcription u, unknown.

In the meantime, Professor K. Abe at the University of Tokyo organized the International Life Science Institute (ILSI) Japan-endowed chair Functional Food Genomics (with Professor Y. Nakai in charge) which aims to explore a new dimension of food science in the form of academia-industry consortium (Nakai etal. 2010). This laboratory has publicized DNA microarray data on soy protein isolate (Tachibana et al. 2005), cocoa as a whole (Matsui et al. 2005), sesamin (Tsuruoka et al. 2005), apple polyphenol (Ohta et al. 2006), grape seed (Sano et al. 2007), royal jelly as a whole (Narita et al. 2006), fructo-oligosaccharide (Fukasawa et al. 2007), vinegar as a whole (Nakano et al. 2004), tomato (Aizawa et al. 2009), and others. What may be extremely interesting would be the data on inhaled linalool as an aroma that reduces a kind of... 

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