Creating views on integrated multidomain data

Rohn, Hendrik; Klukas, Christian; Schreiber, Falk

doi:10.1093/bioinformatics/btr282

Cited by 14 publications

(7 citation statements)

References 20 publications

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“…This method combines structural information, and quantitative gene expression data in their spatio-temporal context thereby providing an intuitive and compact visualization for enhanced visual analysis of large-scale expression analyses. The tool HIVE (Rohn et al, 2011 ) enables biologists to integrate 2D images, expression data, and biological networks, with the underlying VANTED framework (Junker et al, 2006 ) offering further basic network editing and data visualization functionalities. The proposed method is transferable to all -omics domains, thus can be applied for visualization of e.g., metabolomics data in the context of anatomical structures and metabolic networks.…”

Section: Introductionmentioning

confidence: 99%

Visual Analysis of Transcriptome Data in the Context of Anatomical Structures and Biological Networks

Junker¹,

Rohn²,

Schreiber³

2012

Front. Plant Sci.

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The complexity and temporal as well as spatial resolution of transcriptome datasets is constantly increasing due to extensive technological developments. Here we present methods for advanced visualization and intuitive exploration of transcriptomics data as necessary prerequisites in order to facilitate the gain of biological knowledge. Color-coding of structural images based on the expression level enables a fast visual data analysis in the background of the examined biological system. The network-based exploration of these visualizations allows for comparative analysis of genes with specific transcript patterns and supports the extraction of functional relationships even from large datasets. In order to illustrate the presented methods, the tool HIVE was applied for visualization and exploration of database-retrieved expression data for master regulators of Arabidopsis thaliana flower and seed development in the context of corresponding tissue-specific regulatory networks.

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Section: Introductionmentioning

confidence: 99%

Visual Analysis of Transcriptome Data in the Context of Anatomical Structures and Biological Networks

Junker¹,

Rohn²,

Schreiber³

2012

Front. Plant Sci.

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“…This supports the comparative visual analysis of complex flux distributions in an interactive way. Using the HIVE add-on [34] image-based data such as histological cross-sections, microscopy images, photographs and three-dimensional volume data such as NMR and CT data can be displayed in the network context based on a workspace approach and rendered using various 2D-, 3D- and network visualization functions.…”

Section: Methodsmentioning

confidence: 99%

VANTED v2: a framework for systems biology applications

et al. 2012

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BackgroundExperimental datasets are becoming larger and increasingly complex, spanning different data domains, thereby expanding the requirements for respective tool support for their analysis. Networks provide a basis for the integration, analysis and visualization of multi-omics experimental datasets.ResultsHere we present Vanted (version 2), a framework for systems biology applications, which comprises a comprehensive set of seven main tasks. These range from network reconstruction, data visualization, integration of various data types, network simulation to data exploration combined with a manifold support of systems biology standards for visualization and data exchange. The offered set of functionalities is instantiated by combining several tasks in order to enable users to view and explore a comprehensive dataset from different perspectives. We describe the system as well as an exemplary workflow.ConclusionsVanted is a stand-alone framework which supports scientists during the data analysis and interpretation phase. It is available as a Java open source tool from http://www.vanted.org.

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“…The software used here is based on the previous version 4.1 of CELLmicrocosmos PathwayIntegration (CmPI) which integrated traditional 6DOF navigation techniques (see below for the explanation) [13]. A similar approach is HIVE which is based on VANTED [14], [15]. However, the major focus of HIVE was not an intuitive navigation but the integration of a large variety of different data sets.…”

Section: Imentioning

confidence: 99%

Hybrid-Dimensional Visualization and Interaction - Integrating 2D and 3D Visualization with Semi-Immersive Navigation Techniques

Sommer

Wang

et al. 2015

2015 Big Data Visual Analytics (BDVA)

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The integration of 2D visualization and navigation techniques has reached a state where the potential for improvements is relatively low. With 3D-stereoscopy-compatible technology now commonplace not only in research but also in many households, the need for better 3D visualization and navigation techniques has increased. Nevertheless, for the representation of many abstract data such as networks, 2D visualization remains the primary choice. However, often such abstract data is associated with spatial data, thereby increasing the need for combining both 2D and 3D visualization and navigation techniques. We discuss a new hybrid-dimensional approach integrating 2D and 3D (stereoscopic) visualization as well as navigation into a semi-immersive virtual environment. This approach is compared to classical 6DOF navigation techniques. Three scientific as well as educational applications are presented: an educational car model, a plant simulation data exploration, and a cellular model with network exploration, each of these combining spatial with associated abstract data.

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Creating views on integrated multidomain data

Cited by 14 publications

References 20 publications

Visual Analysis of Transcriptome Data in the Context of Anatomical Structures and Biological Networks

Visual Analysis of Transcriptome Data in the Context of Anatomical Structures and Biological Networks

VANTED v2: a framework for systems biology applications

Hybrid-Dimensional Visualization and Interaction - Integrating 2D and 3D Visualization with Semi-Immersive Navigation Techniques

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