Visualization of orthogonal (disjoint) or overlapping datasets is a common task in bioinformatics. Few tools exist to automate the generation of extensively-customizable, high-resolution Venn and Euler diagrams in the R statistical environment. To fill this gap we introduce VennDiagram, an R package that enables the automated generation of highly-customizable, high-resolution Venn diagrams with up to four sets and Euler diagrams with up to three sets. The VennDiagram package offers the user the ability to customize essentially all aspects of the generated diagrams, including font sizes, label styles and locations, and the overall rotation of the diagram. We have implemented scaled Venn and Euler diagrams, which increase graphical accuracy and visual appeal. Diagrams are generated as high-definition TIFF files, simplifying the process of creating publication-quality figures and easing integration with established analysis pipelines. The VennDiagram package allows the creation of high quality Venn and Euler diagrams in the R statistical environment.

https://escholarship.org/content/qt81v9826m/qt81v9826m.pdf?t=qaej4g

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

Xenograft studies indicate that some solid tumors and leukemias are organized as cellular hierarchies sustained by cancer stem cells (CSCs). Despite the promise of the CSC model, its relevance in humans remains uncertain. Here we show that acute myeloid leukemia (AML) follows a CSC model on the basis of sorting multiple populations from each of 16 primary human AML samples and identifying which contain leukemia stem cells (LSCs) using a sensitive xenograft assay. Analysis of gene expression from all functionally validated populations yielded an LSC-specific signature. Similarly, a hematopoietic stem cell (HSC) gene signature was established. Bioinformatic analysis identified a core transcriptional program shared by LSCs and HSCs, revealing the molecular machinery underlying 'stemness' properties. Both stem cell programs were highly significant independent predictors of patient survival and were found in existing prognostic signatures. Thus, determinants of stemness influence the clinical outcome of AML, establishing that LSCs are clinically relevant and not artifacts of xenotransplantation.

Stem cell gene expression programs influence clinical outcome in human leukemia

https://www.linkgroup.hu/docs/13PharmTher.pdf

Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review

Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

/pdf/the-biopax-community-standard-for-pathway-data-sharing-3n69qjgpjh.pdf

The BioPAX community standard for pathway data sharing

High-throughput studies of biological systems are rapidly accumulating a wealth of 'omics'-scale data. Visualization is a key aspect of both the analysis and understanding of these data, and users now have many visualization methods and tools to choose from. The challenge is to create clear, meaningful and integrated visualizations that give biological insight, without being overwhelmed by the intrinsic complexity of the data. In this review, we discuss how visualization tools are being used to help interpret protein interaction, gene expression and metabolic profile data, and we highlight emerging new directions.

/pdf/visualization-of-omics-data-for-systems-biology-550m8ejs1w.pdf

Visualization of omics data for systems biology

https://www.bankofcanada.ca/wp-content/uploads/2018/01/swp2018-3.pdf

Speed Segmentation on Exchanges: Competition for Slow Flow

In 2015, TSX Alpha, a Canadian stock exchange, implemented a speed bump for marketable orders and an inverted fee structure as part of a redesign. We find no evidence that this redesign impacted market-wide measures of trading costs or contributed appreciably to segmenting retail order flow away from other Canadian venues with a maker-taker fee structure. This suggests that Alpha attracts already-segmented flow from venues with fee structures other than maker-taker. Some heavy users of Alpha trade off improvements in fill rates and execution size against mildly larger effective spreads and price impacts. These heavy users also utilize larger market orders and fewer spray orders.

Summary: NAViGaTOR is a powerful graphing application for the 2D and 3D visualization of biological networks. NAViGaTOR includes a rich suite of visual mark-up tools for manual and automated annotation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs. Publication-quality images can be rendered through SVG graphics export. NAViGaTOR supports community-developed data formats (PSI-XML, BioPax and GML), is platform-independent and is extensible through a plug-in architecture. Availability: NAViGaTOR is freely available to the research community from http://ophid.utoronto.ca/navigator/. Installers and documentation are provided for 32- and 64-bit Windows, Mac, Linux and Unix.

/pdf/navigator-network-analysis-visualization-and-graphing-125gfge4u6.pdf

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto.

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Speed Segmentation on Exchanges: Competition for Slow Flow

Speed Segmentation on Exchanges: Competition for Slow Flow

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto.