Compound annotation

Root DE, Flaherty SP, Kelley BP, Stockwell BR. Biological mechanism profiling using an annotated compound library. Chem Biol 2003 10 881-92. 

Cases M, Garcia-Serna R, Hettne K, Weeber M, van der Lei J, Boyer S, Mestres J. Chemical and biological profiling of an annotated compound library directed to the nuclear receptor family. Curr Top Med Chem 2005 5 763-72. 

Molecular Information Systems and Annotated Compound Libraries... 

D.E. Root, S.P. Haherty, B.R Kelley and B.R. Stockwell, Biological mechanism profiling nsing an annotated compound library, Chem. Biol, 2003,10, 881-892. 

Annotate compounds with color coding corresponding to active, inactive, or not tested. 

Fig. 7. Annotating compounds by binning them into classes based on assay result differences, followed by visualization.

Annotate compounds with assay result difference classes. 

An example of the outcome of a Fisher exact test is shown in Figure 4.5. A set of MMoA-annotated compounds were screened for inhibition of TNF-a production in lipopolysaccharide-stimulated THP-1 cells. The TNF-a pathway is well characterized and many known protein nodes, such as IKBKB, were identified in the analysis. Target discovery was consistent with a pathway enrichment analysis and, for each protein, a contigency table was constructed with /i-value and odds ratio calculated. To make sure that the / -values identified were significant when testing many different targets, a Bonferroni correction term - a method used to counteract the problem of multiple comparisons, which occurs when a set of statistical inferences are considered simultaneously - was applied. 

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