Approaches toanalyse and interpret biological profile data

Advances in biotechnologies rapidly increase the number of molecules of a cell which can be observed simultaneously. This includes expression levels of thousands or ten-thousands of genes as well as concentration levels of metabolites or proteins. Such Profile data, observed at different times or at different experimental conditions (e.g., heat or dry stress), show how the biological experiment is reflected on the molecular level. This information is helpful to understand the molecular behaviour and to identify molecules or combination of molecules that characterise specific biological condition (e.g., disease). This work shows the potentials of component extraction algorithms to identify the major factors which influenced the observed data. This can be the expected experimental factors such as the time or temperature as well as unexpected factors such as technical artefacts or even unknown biological behaviour. Extracting components means to reduce the very high-dimensional data to a small set of new variables termed components. Each component is a combination of all original variables. The classical approach for that purpose is the principal component analysis (PCA). It is shown that, in contrast to PCA which maximises the variance only, modern approaches such as independent component analysis (ICA) are more suitable for analysing molecular data. The condition of independence between components of ICA fits more naturally our assumption of individual (independent) factors which influence the data. This higher potential of ICA is demonstrated by a crossing experiment of the model plant Arabidopsis thaliana (Thale Cress). The experimental factors could be well identified and, in addition, ICA could even detect a technical artefact. However, in continuously observations such as in time experiments, the data show, in general, a nonlinear distribution. To analyse such nonlinear data, a nonlinear extension of PCA is used. This nonlinear PCA (NLPCA) is based on a neural network algorithm. The algorithm is adapted to be applicable to incomplete molecular data sets. Thus, it provides also the ability to estimate the missing data. The potential of nonlinear PCA to identify nonlinear factors is demonstrated by a cold stress experiment of Arabidopsis thaliana. The results of component analysis can be used to build a molecular network model. Since it includes functional dependencies it is termed functional network. Applied to the cold stress data, it is shown that functional networks are appropriate to visualise biological processes and thereby reveals molecular dynamics.%%%%Fortschritte in der Biotechnologie ermoglichen es, eine immer grosere Anzahl von Molekulen in einer Zelle gleichzeitig zu erfassen. Das betrifft sowohl die Expressionswerte tausender oder zehntausender Gene als auch die Konzentrationswerte von Metaboliten oder Proteinen. Diese Profildaten verschiedener Zeitpunkte oder unterschiedlicher experimenteller Bedingungen (z.B. unter Stressbedingungen wie Hitze oder Trockenheit) zeigen, wie sich das biologische…