3 research outputs found
Attribute Exploration of Gene Regulatory Processes
This thesis aims at the logical analysis of discrete processes, in particular
of such generated by gene regulatory networks. States, transitions and
operators from temporal logics are expressed in the language of Formal Concept
Analysis. By the attribute exploration algorithm, an expert or a computer
program is enabled to validate a minimal and complete set of implications, e.g.
by comparison of predictions derived from literature with observed data. Here,
these rules represent temporal dependencies within gene regulatory networks
including coexpression of genes, reachability of states, invariants or possible
causal relationships. This new approach is embedded into the theory of
universal coalgebras, particularly automata, Kripke structures and Labelled
Transition Systems. A comparison with the temporal expressivity of Description
Logics is made. The main theoretical results concern the integration of
background knowledge into the successive exploration of the defined data
structures (formal contexts). Applying the method a Boolean network from
literature modelling sporulation of Bacillus subtilis is examined. Finally, we
developed an asynchronous Boolean network for extracellular matrix formation
and destruction in the context of rheumatoid arthritis.Comment: 111 pages, 9 figures, file size 2.1 MB, PhD thesis University of
Jena, Germany, Faculty of Mathematics and Computer Science, 2011. Online
available at http://www.db-thueringen.de/servlets/DocumentServlet?id=1960