Browsing by Author "Nieselt, Kay"

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    GO-Compass: Visual Navigation of Multiple Lists of GO terms
    (The Eurographics Association and John Wiley & Sons Ltd., 2023) Harbig, Theresa; Witte Paz, Mathias; Nieselt, Kay; Bujack, Roxana; Archambault, Daniel; Schreck, Tobias
    Analysis pipelines in genomics, transcriptomics, and proteomics commonly produce lists of genes, e.g., differentially expressed genes. Often these lists overlap only partly or not at all and contain too many genes for manual comparison. However, using background knowledge, such as the functional annotations of the genes, the lists can be abstracted to functional terms. One approach is to run Gene Ontology (GO) enrichment analyses to determine over- and/or underrepresented functions for every list of genes. Due to the hierarchical structure of the Gene Ontology, lists of enriched GO terms can contain many closely related terms, rendering the lists still long, redundant, and difficult to interpret for researchers. In this paper, we present GO-Compass (Gene Ontology list comparison using Semantic Similarity), a visual analytics tool for the dispensability reduction and visual comparison of lists of GO terms. For dispensability reduction, we adapted the REVIGO algorithm, a summarization method based on the semantic similarity of GO terms, to perform hierarchical dispensability clustering on multiple lists. In an interactive dashboard, GO-Compass offers several visualizations for the comparison and improved interpretability of GO terms lists. The hierarchical dispensability clustering is visualized as a tree, where users can interactively filter out dispensable GO terms and create flat clusters by cutting the tree at a chosen dispensability. The flat clusters are visualized in animated treemaps and are compared using a correlation heatmap, UpSet plots, and bar charts. With two use cases on published datasets from different omics domains, we demonstrate the general applicability and effectiveness of our approach. In the first use case, we show how the tool can be used to compare lists of differentially expressed genes from a transcriptomics pipeline and incorporate gene information into the analysis. In the second use case using genomics data, we show how GO-Compass facilitates the analysis of many hundreds of GO terms. For qualitative evaluation of the tool, we conducted feedback sessions with five domain experts and received positive comments. GO-Compass is part of the Tue- Vis Visualization Server as a web application available at https://go-compass-tuevis.cs.uni-tuebingen.de/
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    PTMVision: An Interactive Visualization Platform for Post-Translational Modifications of Proteins
    (The Eurographics Association, 2023) Hackl, Simon; Jachmann, Caroline; Harbig, Theresa; Witte Paz, Mathias; Nieselt, Kay; Gillmann, Christina; Krone, Michael; Lenti, Simone
    In recent years, proteins have been shown to carry many more post-translational modifications (PTMs) than originally thought. The visualization of proteins along with their PTMs facilitates exploration and understanding of the effects of these PTMs on the protein structure, function, and interactions with other proteins. Therefore, we developed PTMVision, an interactive webbased visualization. We combine information about PTMs in the primary sequence with a two-dimensional representation of the protein's tertiary structure using a presence-absence map and a modified contact map that relates PTMs with the spatial arrangement of proteins without the need of a 3D structure. The prototype of PTMVision is part of the TueVis Visualization Server and is available at https://ptmvision-tuevis.cs.uni-tuebingen.de/.
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    VCBM 2021: Frontmatter
    (The Eurographics Association, 2021) Oeltze-Jafra, Steffen; Smit, Noeska N.; Sommer, Björn; Nieselt, Kay; Schultz, Thomas; Oeltze-Jafra, Steffen and Smit, Noeska N. and Sommer, Björn and Nieselt, Kay and Schultz, Thomas
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    Visual Linkage and Interactive Features of Evidente for an Enhanced Analysis of SNP-based Phylogenies
    (The Eurographics Association, 2023) Witte Paz, Mathias; Harbig, Theresa; Varga, Dolores; Kränzle, Eileen; Nieselt, Kay; Gillmann, Christina; Krone, Michael; Lenti, Simone
    Phylogenetic trees of a set of bacterial strains are often used to analyze their evolutionary relationships and they are commonly based on genomic features, such as single nucleotide polymorphisms (SNPs). Evidente - a recently published tool - provides visual and analytical linkage across a phylogenetic tree, SNP data and metadata, and integrates them into one interactive visual analytics platform. In contrast to other approaches, Evidente shows how SNPs agree with the tree structure. Evidente is part of the TueVis server (https://evidente-tuevis.cs.uni-tuebingen.de/). Here, we give an overview of the tasks supported by Evidente. The version of Evidente described in the publication can seamlessly visualize up to 150 strains. Thus, we introduce further enhancements for larger trees, such as data-driven aggregation and semantic zooming.