On text mining to identify gene networks with a special reference to cardiovascular disease

Abstract: The rate at which articles gets published grows exponentially and the possibility to access texts in machine-readable formats is also increasing. The need of an automated system to gather relevant information from text, text mining, is thus growing. The goal of this thesis is to find a biologically relevant gene network for atherosclerosis, themain cause of cardiovascular disease, by inspecting gene cooccurrences in abstracts from PubMed. In addition to this gene nets for yeast was generated to evaluate the validity of using text mining as a method. The nets found were validated in many ways, they were for example found to have the well known power law link distribution. They were also compared to other gene nets generated by other, often microbiological, methods from different sources. In addition to classic measurements of similarity like overlap, precision, recall and f-score a new way to measure similarity between nets are proposed and used. The method uses an urn approximation and measures the distance from comparing two unrelated nets in standard deviations. The validity of this approximation is supported both analytically and with simulations for both Erd¨os-R´enyi nets and nets having a power law link distribution. The new method explains that very poor overlap, precision, recall and f-score can still be very far from random and also how much overlap one could expect at random. The cutoff was also investigated. Results are typically in the order of only 1% overlap but with the remarkable distance of 100 standard deviations from what one could have expected at random. Of particular interest is that one can only expect an overlap of 2 edges with a variance of 2 when comparing two trees with the same set of nodes. The use of a cutoff at one for cooccurrence graphs is discussed and motivated by for example the observation that this eliminates about 60-70% of the false positives but only 20-30% of the overlapping edges. This thesis shows that text mining of PubMed can be used to generate a biologically relevant gene subnet of the human gene net. A reasonable extension of this work is to combine the nets with gene expression data to find a more reliable gene net.