Genes selection

Figure 7.7. Schematic representation of gene selection by compartmentalization. Step 1 An in vitro transcription/translation reaction mixture containing a library of genes linked to a substrate for the reaction being selected is dispersed to form a water-in-oil emulsion with typically one gene per aqueous compartment. Step 2 The genes are transcripted and translated within their compartments. Step 3 Proteins (or RNAs) with enzymatic activities convert the substrate into a product that remains linked to the gene. Compartmentalization prevents the modification of genes in other compartments. Step 4 The emulsion is broken all reactions are stopped and the aqueous compartments are combined. Genes linked to the product are selectively enriched, then amplified, and either characterized (step 5) or linked to the substrate and compartmentalized for further rounds of selection (step 6). (Adapted from [39].)...

Pavlidis P (2003) Using ANOVA for gene selection from microarray studies of the nervous system. Methods 31 282-289. doi S1046202303001579 (pii)... 

Cho JH et al (2004) Gene selection and classification from microarray data using kernel machine. FEBS Lett 571 93-98. doi 10.1016/j.febslet.2004.05.087S001457 9304008142 (pii)... 

Fig. 2. WEB representation of SEVENS database. At the upper part (Fig. 2a), the chromosomal viewer, the phylogenetic map button, and the content search boxes are shown. Using the AND combinations of several conditions, the content search boxes retrieve GPCR genes. Selection of a query gene from these viewers or the list table navigates the user to the gene annotation information page.

Goar, B. Gene, "Selective Gas Treating Produces Better Claus Feeds" Oil and Gas Journal May 5, 1980, 78. 

Pei Q, Lewis L, Sprakes ME, Jones DG, Grahame-Smith DG, Zetterstrom TSC. Serotonergic regulation of mRNA expression of Arc, an immediate early gene selectively localized at neuronal dendrites. Neuropharmacology 2000 39 463-470. 

Figure 4. (a) Reproducibility of the posterior probability (solid line) the estimate of the fold change (dashed line) the f-statistic (dash-dot line) and the signal-to-noise ratio (dotted line) for different sample sizes, for the 1329 genes selected as most differentially expressed by badge on the whole data set (b) the same analysis for the 1329 genes selected as most differentially expressed by the f-statistic. The reproducibility is measured by (1 + p,)/2, where p, is the average correlation between statistics in samples of size n,-(= 6,..., 20). 

Whether strong control of FWER or FDR is appropriate in the analysis of microarrays may depend on how the inference on differential gene expressions is used subsequently. In one form of drug discovery, genes are first screened for differential expressions under normal and disease conditions. Subsequently, nucleotide sequences in the promoter regions of the genes selected in the first step are mined for unusually common sequences (called consensus motifs). Proteins (transcription factors) that bind to these motifs then become candidates for drug compounds to intervene with the disease process. 

The power of the screening or selection method ultimately delineates the extent to which the sequence space can be explored. Screening usually involves the physical separation of mutants identified on some phenotypic change such as colony size or color. It is essentially a brute force approach that is amenable to amplification by robotics and is limited to identification of mutants in a population of transfected bacteria or cells totaling at most one million and more with typically only a few thousand clones each harboring a different mutant gene. Selection takes advantage... 

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