Mapping analysis

Kunkel, E. J., Plavec, L, Nguyen, D., Melrose, J., Rosier, E. S., Kao, L. T., Wang, Y., Hytopoulos, E., Bishop, A. C., Bateman, R., et al. (2004). Rapid structure-activity and selectivity analysis of kinase inhibitors by Bio Map analysis in complex human primary cell-based models. ASSAY Drug Dev. Technol. 2 431-441. 

The transformation by log double-centering has received various names among which spectral mapping [13], logarithmic analysis [14], saturated RC association model [15], log-bilinear model [16] and spectral map analysis or SMA for short [17]. 

Each of the three approaches will be applied in this section to the transformed retention times of the 23 chalcones with eight chromatographic elution methods in Table 31.2. The transformation is defined by the successive operations of logarithms, double-centering and global normalization which is typical for the method of spectral map analysis (SMA) ... 

P.J. Lewi, Spectral map analysis. Analysis of contrasts, especially from log-ratios. Chemom. Intell. Lab. Syst., 5 (1989) 105-116. 

According to Andersen [12] early applications of LLM are attributed to the Danish sociologist Rasch in 1963 and to Andersen himself. Later on, the approach has been described under many different names, such as spectral map analysis [13,14] in studies of drug specificity, as logarithmic analysis in the French statistical literature [15] and as the saturated RC association model [16]. The term log-bilinear model has been used by Escoufier and Junca [ 17]. In Chapter 31 on the analysis of measurement tables we have described the method under the name of log double-centred principal components analysis. 

For a detailed description of spectral map analysis (SMA), the reader is referred to Section 31.3.5. The method has been designed specifically for the study of drug-receptor interactions [37,44]. The interpretation of the resulting spectral map is different from that of the usual principal components biplot. The former is symmetric with respect to rows and columns, while the latter is not. In particular, the spectral map displays interactions between compounds and receptors. It shows which compounds are most specific for which receptors (or tests) and vice versa. This property will be illustrated by means of an analysis of data reporting on the binding affinities of various opioid analgesics to various opioid receptors [45,46]. In contrast with the previous approach, this application is not based on extra-thermodynamic properties, but is derived entirely from biological activity spectra. 

The spectral map shows three distinct poles of specificity. These are respectively the p-receptor (DHM), the 6-receptor (DADLE) and the K-receptor (EKC). The naloxone receptor (NAL) appears to be strongly correlated with the p-receptor (DHM) and, hence, provides little additional information. In spectral map analysis, correlation between variables, as well as similarity between compounds, is evidenced by the proximity of their corresponding symbols. The lines drawn through the three poles of the map represent bipolar axes of contrast. A contrast is defined in this context as a log ratio or, equivalently, as a difference of logarithms. For example, the horizontal axis through the p- and 8-receptors defines the p/6 contrast. Compounds that project on the right side of this axis bind more specifically to the p-receptor, while those that project on the left side possess more... 

Hara, W., Sosnicki, S., and Banno, Y. et al. 2007. Mapping analysis of carotenoid-binding protein of Bombyx mori by restriction fragment length polymorphism. J. Insect Biotechnol. Sericol., 76(3) 149-154. 

Computer-Assisted Drug Receptor Mapping Analysis... 

KARMA is an interactive computer assisted drug design tool that incorporates quantitative structure-activity relationships (QSAR), conformational analysis, and three-dimensional graphics. It represents a novel approach to receptor mapping analysis when the x-ray structure of the receptor site is not known, karma utilizes real time interactive three-dimensional color computer graphics combined with numerical computations and symbolic manipulation techniques from the field of artificial intelligence. 

Greer, J. (1985). Computer skeletonization and automatic electron density map analysis. Method Enzymol. 115, 206-224. 

Some minor discrepancies between theory and experiment on tetrafluoroterephthalonitrile remain to be resolved. The peak densities in the bonds are slightly but systematically lower in the theoretical than in the experimental maps. Analysis of the second moments of the pseudoatoms from the Hirshfeld space partitioning (chapter 6) indicate a greater contraction into the molecular plane in the theoretical than in the experimental study. Whether such discrepancies are artifacts of the refinement model, the result of inter-molecular interactions, or have another origin, is a question of considerable interest. 

Orbital mapping analysis of thermal isomerization of aza- and diaza-bicyclo[2.2.0]hexa-dienes has been carried out (80MI51205). Molecular orbital calculations (MNDO) of a series of bisdehydropyridines showed that the 2-azabicyclo[2.2.0]hexa-l,3,5-triene (125) is the least stable form having a calculated heat of formation of 728.4 kJ mol-1 (77CC539). 

Covell DG, Wallqvist A, Rabow A et al. Molecular classification of cancer unsupervised selforganizing map analysis of gene expression microarray data. Mol Cancer Ther 2003 2 317-332. 

M. D. Jones, L. A. Merewether, C. L. Clogston, and H. S. Lu, Peptide map analysis of recombinant human granulocyte colony stimulating factor elimination of methionine modification and nonspecific cleavages, Anal. Biochem., 276 135 (1994). 

Peptide mapping analysis of proteins Protease Fused-silica capillary [366]... 

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