Journal: Advances and Applications in Bioinformatics and Chemistry : AABC

Article Title: Tools for visualization and analysis of molecular networks, pathways, and -omics data

doi: 10.2147/AABC.S63534

Figure Lengend Snippet: Visualization of differential expression data on the Glycolysis pathway using different software packages. Notes: ( A ) KEGG Mapper and KEGGViewer were used to render -omics data on the KEGG Glycolysis pathway. Upregulated genes are shown in yellow, and downregulated genes are highlighted in blue. ( B ) PathVisio was used to visualize -omics data on the Glycolysis pathway from WikiPathways. Upregulated genes are colored in red shades, and downregulated genes are shown in green shading. PathVisio is able to combine two datasets on the same pathway map. ( C ) The Reactome analysis toolbox was used to visualize -omics data on the Glycolysis pathway. Upregulated genes are highlighted in yellow, and downregulated genes are highlighted in blue.

Article Snippet: KEGG-based Pathway Visualization Tool for Complex Omics Data , Web , KEGG.

Techniques: Quantitative Proteomics, Software

Journal: Frontiers in Neuroinformatics

Article Title: Fiberweb: Diffusion Visualization and Processing in the Browser

doi: 10.3389/fninf.2017.00054

Figure Lengend Snippet: Fiber bundle (part of the corpus callosum), result of the real-time tractography, with the initialization box (red) in the mid-sagittal slice of the CC and the following parameters: angle threshold of 50°, fiber length minimum of 10 mm and maximum of 200 mm, FA threshold of 0.1, a step size of 0.5 mm, 10 seeds per axis and a puncture value (g) of 0.2.

Article Snippet: In this article, Fiberweb, a new browser-based medical dMRI tractography visualization tool, was presented.

Techniques:

Journal: Frontiers in Neuroinformatics

Article Title: Fiberweb: Diffusion Visualization and Processing in the Browser

doi: 10.3389/fninf.2017.00054

Figure Lengend Snippet: Various bundles resulting from probabilistic tractography (real-time in the Fiberweb vs offline). Dice coefficients are: CST (0.865), CC (0.928), and AF (0.811). The yellow arrows show the location of seeding regions. (A) Results of the Fiberweb algorithm for the corticospinal tract. (B) Results of the offline algorithm for the corticospinal tract. (C) Results of the Fiberweb algorithm for the corpus callosum. (D) Results of the offline algorithm for the corpus callosum. (E) Results of the Fiberweb algorithm for the arcuate fasciculus. (F) Results of the offline algorithm for the arcuate fasciculus.

Article Snippet: In this article, Fiberweb, a new browser-based medical dMRI tractography visualization tool, was presented.

Techniques:

Journal: Frontiers in Neuroinformatics

Article Title: Fiberweb: Diffusion Visualization and Processing in the Browser

doi: 10.3389/fninf.2017.00054

Figure Lengend Snippet: CST bundles resulting from probabilistic tractography, with a varying uncertainty percentage threshold. (A) Results of the Fiberweb algorithm for 100% uncertainty. (B) Results of the Fiberweb algorithm for 50% uncertainty. (C) Results of the Fiberweb algorithm for 35% uncertainty. (D) Results of the Fiberweb algorithm for 25% uncertainty. (E) Results of the Fiberweb algorithm for 15% uncertainty. (F) Results of the Fiberweb algorithm for 0% uncertainty.

Article Snippet: In this article, Fiberweb, a new browser-based medical dMRI tractography visualization tool, was presented.

Techniques:

Journal: Molecular Brain

Article Title: Broad proteomics analysis of seeding-induced aggregation of α-synuclein in M83 neurons reveals remodeling of proteostasis mechanisms that might contribute to Parkinson’s disease pathogenesis

doi: 10.1186/s13041-024-01099-1

Figure Lengend Snippet: Proteomic analysis in the insoluble fraction of α-syn PFF treated M83 neurons. A M83 neurons treated with α-syn PFFs or PBS for 14± 1 and 21± 1 days were sequentially extracted with 1% Triton X-100 followed by 2% SDS. Western blot analysis showed significant enrichment of pS129 α-syn in the Triton X-100 insoluble fraction from PFF treated neuron samples. With PBS treatment, α-syn was extracted in 1% Triton X-100 fraction. B Insoluble fractions analyzed by Mass spectrometry identified 92 proteins that were changed in the total proteome with PFF treatment at logFC cutoff of ≥ 0.25. An enrichment analysis using metascape for these 92 proteins was performed, which identified membrane/vesicle trafficking, autophagy, endocytosis, and exocytosis mechanisms. C Based on a stringent cutoff of 0.999 in CPDB, a first order network of these 92 proteins including 1640 proteins and 4,738 interactors was generated. Based on this, a zero-order network was established using the internally developed network-based visual analytics tool to identify enriched pathways which are shown in the figure. The most enriched pathways in this network included the mitochondrial pathway, translation, ubiquitin related, lysosome, unfolded protein response, vesicle trafficking and mRNA splicing

Article Snippet: Visualization of this network containing 1328 proteins and 3621 interactions using internally developed network-based visual analytics tool identified modules involved in proteostasis.

Techniques: Western Blot, Mass Spectrometry, Membrane, Generated, Ubiquitin Proteomics

Journal: Advances and Applications in Bioinformatics and Chemistry : AABC

Article Title: Tools for visualization and analysis of molecular networks, pathways, and -omics data

doi: 10.2147/AABC.S63534

Figure Lengend Snippet: Visualization of differential expression data on the Glycolysis pathway using different software packages. Notes: ( A ) KEGG Mapper and KEGGViewer were used to render -omics data on the KEGG Glycolysis pathway. Upregulated genes are shown in yellow, and downregulated genes are highlighted in blue. ( B ) PathVisio was used to visualize -omics data on the Glycolysis pathway from WikiPathways. Upregulated genes are colored in red shades, and downregulated genes are shown in green shading. PathVisio is able to combine two datasets on the same pathway map. ( C ) The Reactome analysis toolbox was used to visualize -omics data on the Glycolysis pathway. Upregulated genes are highlighted in yellow, and downregulated genes are highlighted in blue.

Article Snippet: The KEGG-based Pathway Visualization Tool for Complex Omics Data is another practical, user-friendly method to visualize expression data on KEGG pathways.

Techniques: Quantitative Proteomics, Software

Journal: Archives of Toxicology

Article Title: Molecular basis of mood and cognitive adverse events elucidated via a combination of pharmacovigilance data mining and functional enrichment analysis

doi: 10.1007/s00204-020-02788-1

Figure Lengend Snippet: Major elements of the workflow applied to the analysis of pharmacovigilance reports and its subsequent linking with the basic biological knowledge. a Mood and cognitive MedDRA terms used for the selection of mood- and cognitive-related AEs. b Graphical representation of the two approaches used to identify the pathways and mechanisms of action leading to Mood and Cognitive AEs. Expert curation was carried out using PubMed and the Biovista Vizit tool

Article Snippet: Biovista Vizit is a visual bibliographic PubMed-based search tool that helps researchers and medical practitioners explore the existing knowledge of a biomedical domain, discover non-obvious links between entities (e.g. genes, pathways, drugs, etc.), visualize biological interconnections and communicate findings with peers ( https://www.biovista.com/vizit/ ).

Techniques: Selection