Array Express

There are many products based on these life sciences standards, such as the aforementioned gene expression standard that is used in Rosetta Merck s Resolver product and the European Bioinformatics Institute s (EBI) Array-Express database. The LECIS (Laboratory Equipment Control Interface Specification) standard is used by Creon as part of their Q-DIS data standard support (note that one of the authors was the finalization task force chairperson for this standard). 

Hilsenbeck SG et al. Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J Natl Cancer Inst 1999 91 453-459. 

HILSENBECK, S.G., FRIEDRICHS, W.E., SCHIFF, R., O CONNELL, P., HANSEN, R.K., OSBORNE, C.K., FUQUA, S.A., Statistical analysis of array expression data as applied to the problem of tamoxifen resistance, J. Natl. Cancer Inst., 1999,91,453-459. 

Iazzetti G, Calabro V, Saviozzi S, Weisz A, Lania L, Calogero R, BSC A clustering program for DNA array expression data, Proceedings of Biocomp, 2001, Siena, 2001. http //obelix.bio.uniroma2.it/www/abstr 2001. html iazzetti... 

Array Express Database. Available at http //www.ebi.ac.uk/microarray-as/ae/. Accessed 20 Jan 2009... 

Public repositories that adhere to academic or industry standards and are designed to be used by many analysis applications and groups. A good example of this is the Gene Expression Omnibus from the NCBI (http // www.ncbi.nlm.nih.gov) (75) or Array Express from the EBI (http //www. ebi.ac.uk) (76). 

Keywords Protein Array, Expression Profiling, Automation, Serum Screening, Antibody Profiling, Protein Purification... 

Because of these complexities, we will start by describing a simplified Array-Express model - ArrayExpressB, after which we will add the details of the Ar-rayExpressC model. Some users may not need to implement the ArrayExpressC model for their particular purposes. We encourage users to assess whether the ArrayExpressB model is sufficient or not (data structured according to the ArrayExpressB model can be later imported into the ArrayExpressC model compliant database). Also, a whole range of intermediate models between the two extremes is possible. In fact, these models should be critically assessed by users and adjusted to the particular needs of their laboratories. 

Several public databases serve mieroarray data and include tools for mieroarray analysis, including the Stanford Mieroarray Database [165], the RIKEN Expression Array Database [166], and Array Express at the European Bioinformatics Institute [167]. 

Li, G, and Wong, W.H. 2001. Model-based analysis of oligonucleotide arrays Expression index computation and outlier detection. Proc Natl Acad Sci USA 98 31-36. 

A fundamental characteristic of spatially periodic systems is the existence of a group of translational symmetry operations, by means of which the repeating pattern may be brought into self-coincidence. The translational symmetry of the array, expressing its invariance with respect to parallel displacements in different directions is represented by a lattice. This lattice consists of an array of evenly spaced points (Fig. 3-13), such that the structural elements appear the same and in the same orientation when viewed from each and every one of the lattice points. Another important property of spatially periodic arrays is the existence of two characteristic length scales, corresponding to the average microscopic distance between lattice... 

For the noiseless case, X(ixjk) = A(A/A) 1A/X(/x/X) showing that X can be expressed on the truncated basis A. The regression onto A, W, is an array of size P x JK which holds the coefficients of X expressed with respect to the truncated basis A in the first mode. For all three modes considered simultaneously the coefficient matrix is the array expressed in terms of all the new bases A in the first mode, B in the second mode, and C in the third mode. This array reads... 

Mateos, A. Dopazo J. Jansen, R. Tu, Y. Gerstein, M Stolovitzky, G. (2002). Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. Genome Res. Vol. 12, pp. 1703-1715. 

Note the use of parenthesis around the logical function. Without these around the And operation the expression will be incorrectly evaluated. Both these expressions contain strings of characters enclosed in double quotes that are used to represent bit patterns. These examples illustrate binary representations but octal and hexadecimal formats may also be used (see Box 5.5). Using the concatenation operator to construct array expressions is only one approach. It is also possible to use aggregate expressions that take the form ... 

---