<p>The main objective of the reported study was to investigate how biomedical ontologies, logically structured representations of various aspects of the biomedical reality, can help researchers in analyzing experimental data. The dissertation reports two attempts to construct tools for the analysis of high-throughput experimental results using explicit domain knowledge representations. Furthermore, integrative efforts made by the community of Open Biomedical Ontologies (OBO), in which the author has participated, are reported, and a framework for consistently connecting the Gene Ontology (GO) with the Taxonomy of Species is proposed and discussed.</p>

The main objective of the reported study was to investigate how biomedical ontologies, logically structured representations of various aspects of the biomedical reality, can help researchers in analyzing experimental data. The dissertation reports two attempts to construct tools for the analysis of high-throughput experimental results using explicit domain knowledge representations. Furthermore, integrative efforts made by the community of Open Biomedical Ontologies (OBO), in which the author has participated, are reported, and a framework for consistently connecting the Gene Ontology (GO) with the Taxonomy of Species is proposed and discussed.

Cancer is a very complex genetic disease driven by combinations of mutated genes. This complexity strongly complicates the identification of driver genes and puts enormous challenges to reveal how they influence cancerogenesis, prognosis or therapy response. Thousands of molecular profiles of the major human types of cancer have been measured over the last years. Apart from well-studied frequently mutated genes, still only little is known about the role of rarely mutated genes in cancer or the interplay of mutated genes in individual cancers. Gene expression and mutation profiles can be measured routinely, but computational methods for the identification of driver candidates along with the prediction of their potential impacts on downstream targets and clinically relevant characteristics only rarely exist. Instead of only focusing on frequently mutated genes, each cancer patient should better be analyzed by using the full information in its cancer-specific molecular profiles to improve the understanding of cancerogenesis and to more precisely predict prognosis and therapy response of individual patients. This requires novel computational methods for the integrative analysis of molecular cancer data. A promising way to realize this is to consider cancer as a disease of cellular networks. Therefore, I have developed a novel network-based approach for the integrative analysis of molecular cancer data over the last years. This approach directly learns gene regulatory networks form gene expression and copy number data and further enables to quantify impacts of altered genes on clinically relevant downstream targets using network propagation. This habilitation thesis summarizes the results of seven of my publications. All publications have a focus on the integrative analysis of molecular cancer data with an overarching connection to the newly developed network-based approach. In the first three publications, networks were learned to identify major regulators that distinguish characteristic gene expression signatures with applications to astrocytomas, oligodendrogliomas, and acute myeloid leukemia. Next, the central publication of this habilitation thesis, which combines network inference with network propagation, is introduced. The great value of this approach is demonstrated by quantifying potential direct and indirect impacts of rare and frequent gene copy number alterations on patient survival. Further, the publication of the corresponding user-friendly R package regNet is introduced. Finally, two additional publications that also strongly highlight the value of the developed network-based approach are presented with the aims to predict cancer gene candidates within the region of the 1p/19q co-deletion of oligodendrogliomas and to determine driver candidates associated with radioresistance and relapse of prostate cancer. All seven publications are embedded into a brief introduction that motivates the scientific background and the major objectives of this thesis. The background is briefly going from the hallmarks of cancer over the complexity of cancer genomes down to the importance of networks in cancer. This includes a short introduction of the mathematical concepts that underlie the developed network inference and network propagation algorithms. Further, I briefly motivate and summarize my studies before the original publications are presented. The habilitation thesis is completed with a general discussion of the major results with a specific focus on the utilized network-based data analysis strategies. Major biologically and clinically relevant findings of each publication are also briefly summarized.

Dizertační práce se zabývá predikcí vysokodimenzionálních dat genových expresí. Množství dostupných genomických dat významně vzrostlo v průběhu posledního desetiletí. Kombinování dat genových expresí s dalšími daty nachází uplatnění v mnoha oblastech. Například v klinickém řízení rakoviny (clinical cancer management) může přispět k přesnějšímu určení prognózy nemocí. Hlavní část této dizertační práce je zaměřena na kombinování dat genových expresí a klinických dat. Používáme logistické regresní modely vytvořené prostřednictvím různých regularizačních technik. Generalizované lineární modely umožňují kombinování modelů s různou strukturou dat. V dizertační práci je ukázáno, že kombinování modelu dat genových expresí a klinických dat může vést ke zpřesnění výsledku predikce oproti vytvoření modelu pouze z dat genových expresí nebo klinických dat. Navrhované postupy přitom nejsou výpočetně náročné.  Testování je provedeno nejprve se simulovanými datovými sadami v různých nastaveních a následně s~reálnými srovnávacími daty. Také se zde zabýváme určením přídavné hodnoty microarray dat. Dizertační práce obsahuje porovnání příznaků vybraných pomocí klasifikátoru genových expresí na pěti různých sadách dat týkajících se rakoviny prsu. Navrhujeme také postup výběru příznaků, který kombinuje data genových expresí a znalosti z genových ontologií.