Clustering of [Ca²⁺]ᵢ Traces for Studying Calcium Signaling on a Single-cell Level

In T cells intracellular free calcium ions play an important role as universal secondary messengers. Several studies have shown that these signals are the key to cellular processes, for example apoptosis, synapse formation, gene expression and even activation and differentiation of T cells. Alongside the variety of functions as second messenger it is also associated with several forms of diseases and dysfunctions. Examples are inadequately strong immune responses, which can lead to allergies or diabetes, or autoimmune affections such as the Bruton-Syndrom (XLA). Hence, in order to gain a deeper understanding of the immune system it is necessary to investigate the impact of certain biomolecules to calcium signals. For detailed investigations of biomolecules and their calcium pathways, biologists and biophysicists, at the Center for advanced Bioanalysis (CBL) in Linz, developed an image-based method for measuring calcium signals, during T cell activation, on a single-cell level. To identify similar impacts of biomolecules, the signals are grouped according to the structural characteristics. The methods that were in use at the CBL previously did not deliver sufficiently detailed results. In the context of this master thesis, the Institute for Bioinformatics in Linz and the CBL formed a cooperation and developed a new way of clustering these traces. Therefore we developed a novel similarity measure which captures the whole-time-scale behavior of the signal and also takes care of time Variations in signal start. With the clustering algorithm "Affinity Propagation" we were able to identify several similar duster structures in a first case study. Furthermore, statistical methods were implemented, which made it possible to acquire an extensive overview and visualization of this case study which can now be examined from an entirely new perspective. Etc.