Chemical genomic profiling of biological networks using graph theory and combinations of small molecule perturbations

Journal of the American Chemical Society

Volumn 125, Issue 35, 2003, Pages 10543-10545

  Haggarty, Stephen J ^a   Clemons, Paul A ^a   Schreiber, Stuart L ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL POLARITY; CHEMICAL ANALYSIS; GENE DELETION; GENOME IMPRINTING; MOLECULAR INTERACTION; OPTICAL DENSITY; PROTEIN ANALYSIS; RNA ANALYSIS; SAMPLING; STRAIN DIFFERENCE; THEORY;

COMPUTER GRAPHICS; DATA DISPLAY; DATA INTERPRETATION, STATISTICAL; GENE DELETION; GENE EXPRESSION PROFILING; SACCHAROMYCES CEREVISIAE;

EID: 0041353959     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja035413p     Document Type: Article

References (27)

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10. 2 - N)/2 unique combinations (in duplicate) and N single treatments (on the diagonal of the matrix).
11. Stock solutions of small molecules in DMSO were first diluted as appropriate (see Supporting Information, Table S1) in yeast media and then pipetted into the wells of 96-well plates.
12. Cultures were grown in 1% yeast extract (Difco), 2% peptone (Difco), and 2% dextrose (Sigma) added to autoclaved water.
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18. SMPs were chosen on the basis of their bioactivity pattern in a variety of yeast screens. See Supporting Information, Table SI, for details about concentrations and solubility.
19. Replicates within the profiling matrix where only one of the two wells showed no or reduced growth (frequency of 1.3% of total observations) were not considered as edges (see Supporting Information, Table S2).
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26. Eigenvalue spectra and eigenvectors of normalized Laplacian matrices were computed using MATLAB 6 (MathWorks, Inc.) and the commands E = eig(LAP); [V,E] = eig(LAP), where E represents the matrix of eigenvalues, V represents the matrix of eigenvectors, and LAP represents the normalized Laplacian matrix.
27. Hierarchical clustering and principal component analysis was performed using XLStat (Addinsoft) and Excel (Microsoft). Three-dimensional visualizations were plotted using Spotfire DecisionSite (Spotfire, Inc).