Genomics toolbox

Genome-wide characterization of the lignification toolbox in Arabidopsis, Plant Physiol. 133 1051-1071. 

Raes, J., Rohde, A., Christensen, J. EL, Van de Peer, Y., and Boeijan, W., 2003, Genome-wide characterization of the lignification toolbox in Arabidopsis, Plant Physiol. 133 1051-1071. 

Table 7.1). The analysis of both microbial genome and transcriptome represents a rich molecular toolbox for the study of microbial community in food matrices. 

Fig. 5 SOM outputs of genome transcriptional changes from MCF7 cells selected with A-C high concentrations of Dox alone, D Dox formulated with 0.001% P85, E P85 alone, and F low concentration of Dox alone. The data analysis was performed by Li Xiao (Ep-pley Institute for Research in Cancer, UNMC) using MATLAB software (The MathWorks, Inc.) and SOM toolbox for MATLAB (http //www.cis.hut.fi/projects/somtoolbox)...

Jensen P, Lutz K, Papin J (2011) Tiger toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC Syst Biol 5 147 Jevremovic D, Trinh CT, Srienc F, Boley D (2010) On algebraic properties of extreme pathways in metabolic networks. J Comput Biol 17 107-119... 

Example The function of metalloproteins critically depends on their interaction with a metal, e.g., Cu, Zn, Fe, Mo, or metalloid such as Se or As. The living cell not only depends on its genome and proteome, but also on its metallome, i.e., the distribution of those elements among different biomolecules. The complexity of speciation analysis demands for a combined approach of separation techniques and different methods of mass spectrometry. This is best illustrated by the metallomics toolbox that reflects the current understanding of how the metallome can be explored (Fig. 15.1) [21]. 

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