Microarray complexity

The amount of genomic information on a microarray is expressed as microarray complexity, calculated as the product of the number of unique sequences, times their average length in nucleotide, i.e. ... 

Microarray complexity = Number of unique sequences x Average length The complexity of a microarray is often expressed as a fnnction of the size of genome represented in terms of a genome equivalent, i.e. ... 

Genome equivalent = Microarray complexity/Genome size... 

Microarray experiments generate large and complex data sets that constitute e.g. lists of spot intensities and intensity ratios. Basically, the data obtained from microarray experiments provide information on the relative expression of genes corresponding to the mRNA sample of interest. Computational and statistical tools are required to analyze the large amount of data to address biological questions. To this end, a variety of analytical platforms are available, either free on the Web or via purchase of a commercially available product. 

Additional information on biomarker approaches and new technologies, such as microarray assays, developed to address complex pollution problems... 

Shalon, D., Smith, S. J., and Brown, P. O. (1996). A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639-645. 

The second part of this paper considers genetic chips or microarrays as one recent tool developed to deal with the reappreciated complexity of... 

Chamber J et al. DNA microarrays of the complex human cytomegalovirus genome profiling kinetic class with drug sensitivity of viral gene expression. J Virol 1999 73 5757-5766... 

Amundson SA et al. Fluorescent cDNA microarray hybridisation reveals complexity and heterogeneity of cellular geno-toxic stress responses. Oncogene 1999 18 3666-3672. 

Figure 10.1 Experimental schemes for microarray analysis. All experimental schemes start with a separation step of the cell lysate by velocity sedimentation in a sucrose gradient (top scheme). Collection of the desired fractions is assisted by a continuous ultraviolet (UV) reading of the gradient (an example of such UV reading is shown in each section). This allows determination of the sedimentation position of the 40S, 60S, 80S, and polyribosomal complexes (2,3, and more).Three general ways for fraction collection and analysis are presented (sections A, B, and C) (A) Collection of two fractions (free and polysomes) and direct comparison between them, with the free mRNA fraction labeled with green dye and the polysome fraction labeled with red dye. (B) Collection of two fractions and indirect comparison between them by utilizing an unfractionated reference RNA. (C) Collection of multiple fractions (four in this case), where each fraction is compared to an unfractionated reference sample. The blue arrows indicate the addition of spike-in RNA to each fraction and to the reference RNA.

Johannes, G., Carter, M. S., Eisen, M. B., Brown, P. O., and Samow, P. (1999). Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc. Natl. Acad. Sci. USA 96, 13118—13123. 

A similar type of biotin-dendritic multimer also was used to boost sensitivity in DNA microarray detection by 100-fold over that obtainable using traditional avidin-biotin reagent systems (Stears, 2000 Striebel et al., 2004). With this system, a polyvalent biotin dendrimer is able to bind many labeled avidin or streptavidin molecules, which may carry enzymes or fluorescent probes for assay detection. In addition, if the biotinylated dendrimer and the streptavidin detection agent is added at the same time, then at the site of a captured analyte, the biotin-dendrimer conjugates can form huge multi-dendrimer complexes wherein avidin or streptavidin detection reagents bridge between more than one dendrimer. Thus, the use of multivalent biotin-dendrimers can become universal enhancers of DNA hybridization assays or immunoassay procedures. 

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