Bioinformatik, Biostatistik und Systemmodelle CLA supplementierter Milchkühe
Final Report Abstract
Our project is subproject 8 of a joint paket project on “Einfluss einer gestaffelten Supplementation mit pansenstabilen konjugierten Linolsäurena (CLA) auf physiologische und pathophysiologische Prozesse bei Milchkühen sowie auf die Produktsicherheit”. The overall project was on handling a large cohort of cows and to investigate the effect of different levels of CLA supplementation with various experimental measurements on various tissues and output parameters of the cows. Intended results were findings on the health and disease of the cows under treatment as well as on product, i.e. milk and meat, security. The bioinformatics subproject TP8 supported partners in the CLA project to demonstrate the feasibility of bioinformatics support for a large and difficult real world research problem: namely managing, curating, and integrating the data from various subprojects working on the same animal cohort in order to optimally exploit the heterogeneous data and to facilitate publication of the findings. Moreover, the project should develop new innovative bioinformatics methods based on the research questions and problems posed in the packet project. In particular, the goal of TP8 was to facilitate an integrative analysis of the measurements across the various CLA subprojects and to enable an integrative systems biology modeling of the results. Unfortunately, the consistency and overlap of the factors and molecular species jointly measured in different projects as well as their corresponding time dependent resolution were too restricted to enable a detailed integration of the respective results from the subprojects. Therefore, a overarching systems modeling of the data so far generated in the CLA project remains currently infeasible. On the other hand, T8 led to the development of quite a number of bioinformatics methods with application to research questions posed in the CLA project. Three major bioinformatic fields have been addressed, namely the processing and analysis of the heterogeneous CLA datasets (G1.1, G1.2, G1.3 and G1.4), the intensive curation and integration of CLA related knowledge (G1.5, G1.6, G2.1 and G2.3) as well as the modeling of this knowledge and the model based analysis of experimental results (G3.1, G3.2, G3.3 and G3.4). As initially proposed, we thereby developed the bioinformatic methodology and infrastructure to compile widespread knowledge and to integrate it with experimental results to enable the construction of systems biology models. Several of the methods will be further developed in forthcoming and already started projects (such as PHAENOMICS). Large efforts have been invested in TP8 to standardize and curate the various data of the other subprojects and to make them available via an integrated exchange and analysis platform. Again several tools and visualizations have been developed, which will be followed on in other projects such as PHAENOMICS (for farm animals) and in a planned SFB on atherosclerosis via a transfer to the human system).
