原创力文档a systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants系统方法来识别相关基因的目标失去颜色的色素在植物.pdfVIP
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a systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants系统方法来识别相关基因的目标失去颜色的色素在植物
Clark and Verwoerd BMC Bioinformatics 2011, 12:343
/1471-2105/12/343
RESEARCH ARTICLE Open Access
A systems approach to identifying correlated
gene targets for the loss of colour pigmentation
in plants
*
Sangaalofa T Clark and Wynand S Verwoerd
Abstract
Background: The numerous diverse metabolic pathways by which plant compounds can be produced make it
difficult to predict how colour pigmentation is lost for different tissues and plants. This study employs
mathematical and in silico methods to identify correlated gene targets for the loss of colour pigmentation in plants
from a whole cell perspective based on the full metabolic network of Arabidopsis. This involves extracting a self-
contained flavonoid subnetwork from the AraCyc database and calculating feasible metabolic routes or elementary
modes (EMs) for it. Those EMs leading to anthocyanin compounds are taken to constitute the anthocyanin
biosynthetic pathway (ABP) and their interplay with the rest of the EMs is used to study the minimal cut sets
(MCSs), which are different combinations of reactions to block for eliminating colour pigmentation. By relating the
reactions to their corresponding genes, the MCSs are used to explore the phenotypic roles of the ABP genes, their
relevance to the ABP and the impact their eliminations would have on other processes in the cell.
Results: Simulation and prediction results of the effect of different MCSs for eliminating colour pigmentation
correspond with existing experimental observations. Two examples are: i) two MCSs which require the
simultaneous suppression of genes DFR and ANS to eliminate colour pigmentation, correspond to observational
results of the same genes being co-regulated for eliminating floral pigmentation in Aquilegia and; ii) the impact of
another MCS requiring CHS suppr
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