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- Steinfath, Matthias, et al.
(författare)
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Integrated data analysis for genome-wide research
- 2007
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Ingår i: Plant Systems Biology. - Switzerland : Springer. - 9783764374396 ; , s. 309-29
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Bokkapitel (refereegranskat)abstract
- Integrated data analysis is introduced as the intermediate level of a systems biology approach to analyse different 'omics' datasets, i.e., genome-wide measurements of transcripts, protein levels or protein-protein interactions, and metabolite levels aiming at generating a coherent understanding of biological function. In this chapter we focus on different methods of correlation analyses ranging from simple pairwise correlation to kernel canonical correlation which were recently applied in molecular biology. Several examples are presented to illustrate their application. The input data for this analysis frequently originate from different experimental platforms. Therefore, preprocessing steps such as data normalisation and missing value estimation are inherent to this approach. The corresponding procedures, potential pitfalls and biases, and available software solutions are reviewed. The multiplicity of observations obtained in omics-profiling experiments necessitates the application of multiple testing correction techniques.
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| 2. |
- Andorf, Sandra, et al.
(författare)
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Towards systems biology of heterosis : a hypothesis about molecular network structure applied for the Arabidopsis metabolome
- 2009
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Ingår i: EURASIP Journal on Bioinformatics and Systems Biology. - Germany : Springer. - 1687-4145 .- 1687-4153.
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Tidskriftsartikel (refereegranskat)abstract
- We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with increasing heterozygosity--a known phenomenon in the literature.
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| 3. |
- Schauer, Nicolas, et al.
(författare)
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Mode of inheritance of primary metabolic traits in tomato
- 2008
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Ingår i: The Plant Cell. - Rockville, USA : American Society of Plant Biologist. - 1040-4651 .- 1532-298X. ; 20:3, s. 509-23
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Tidskriftsartikel (refereegranskat)abstract
- To evaluate components of fruit metabolic composition, we have previously metabolically phenotyped tomato (Solanum lycopersicum) introgression lines containing segmental substitutions of wild species chromosome in the genetic background of a cultivated variety. Here, we studied the hereditability of the fruit metabolome by analyzing an additional year's harvest and evaluating the metabolite profiles of lines heterozygous for the introgression (ILHs), allowing the evaluation of putative quantitative trait locus (QTL) mode of inheritance. These studies revealed that most of the metabolic QTL (174 of 332) were dominantly inherited, with relatively high proportions of additively (61 of 332) or recessively (80 of 332) inherited QTL and a negligible number displaying the characteristics of overdominant inheritance. Comparison of the mode of inheritance of QTL revealed that several metabolite pairs displayed a similar mode of inheritance of QTL at the same chromosomal loci. Evaluation of the association between morphological and metabolic traits in the ILHs revealed that this correlation was far less prominent, due to a reduced variance in the harvest index within this population. These data are discussed in the context of genomics-assisted breeding for crop improvement, with particular focus on the exploitation of wide biodiversity.
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