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The interpretation of data-driven experiments in genomics often involves a search for biological categories that are enriched for the responder genes identified by the experiments. However, knowledge bases such as the Gene Ontology (GO) contain hundreds or thousands of categories with very high overlap between categories. Thus, enrichment analysis performed(More)
UNLABELLED The Ontologizer is a Java application that can be used to perform statistical analysis for overrepresentation of Gene Ontology (GO) terms in sets of genes or proteins derived from an experiment. The Ontologizer implements the standard approach to statistical analysis based on the one-sided Fisher's exact test, the novel parent-child method, as(More)
BACKGROUND Until now, only imatinib and sunitinib have proven clinical benefit in patients with gastrointestinal stromal tumours (GIST), but almost all metastatic GIST eventually develop resistance to these agents, resulting in fatal disease progression. We aimed to assess efficacy and safety of regorafenib in patients with metastatic or unresectable GIST(More)
We propose an improved statistic for detecting over-represented Gene Ontology (GO) annotations in gene sets. While the current methods treats each term independently and hence ignores the structure of the GO hierarchy, our approach takes parent-child relationships into account. Over-representation of a term is measured with respect to the presence of its(More)
The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes(More)
MOTIVATION High-throughput experiments such as microarray hybridizations often yield long lists of genes found to share a certain characteristic such as differential expression. Exploring Gene Ontology (GO) annotations for such lists of genes has become a widespread practice to get first insights into the potential biological meaning of the experiment. The(More)
T cells with variable region Vdelta1 gammadelta T cell receptors (TCRs) are distributed throughout the human intestinal epithelium and may function as sentinels that respond to self antigens. The expression of a major histocompatibility complex (MHC) class I-related molecule, MICA, matches this localization. MICA and the closely related MICB were recognized(More)
MOTIVATION Several recent studies have demonstrated the effectiveness of resequencing and single nucleotide variant (SNV) detection by deep short-read sequencing platforms. While several reliable algorithms are available for automated SNV detection, the automated detection of microindels in deep short-read data presents a new bioinformatics challenge. (More)
We present a real-time multi-sensor architecture for video-based pedestrian detection used within a road side unit for intersection assistance. The entire system is implemented on available PC hardware, combining a frame grabber board with embedded FPGA and a graphics card into a powerful processing network. Giving classification performance top priority,(More)
Phenotype analyses, e.g. investigating metabolic processes, tissue formation, or organism behavior, are an important element of most biological and medical research activities. Biomedical researchers are making increased use of ontological standards and methods to capture the results of such analyses, with one focus being the comparison and analysis of(More)