Pathview Web: user friendly pathway visualization and data integration.
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TLDR
The Pathview Web server is developed, to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources, and presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data.Abstract:
Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/.read more
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Imbalance of gut microbiome and intestinal epithelial barrier dysfunction in patients with high blood pressure.
Seungbum Kim,Ruby Goel,Ashok V. Kumar,Yanfei Qi,Gil Lobaton,Koji Hosaka,Mohammed Mohammed,Eileen M. Handberg,Elaine M. Richards,Carl J. Pepine,Mohan K. Raizada +10 more
TL;DR: The hypotheses that high blood pressure patients have distinct gut microbiomes and that gut-epithelial barrier function markers and microbiome composition could predict systolic BP (SBP) were tested, supporting the conclusion that intestinal barrier dysfunction and microbiome function are linked to HTN in humans.
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METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation
Luca Pandolfini,Isaia Barbieri,Andrew J. Bannister,Alan G. Hendrick,Byron Andrews,Natalie A. Webster,Pierre Murat,Pia Mach,Rossella Brandi,Samuel Robson,Valentina Migliori,Andrej Alendar,Mara D'Onofrio,Shankar Balasubramanian,Tony Kouzarides +14 more
TL;DR: The results identify METTL1-dependent N7-methylation of guanosine as a new RNA modification pathway that regulates miRNA structure, biogenesis, and cell migration.
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RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs
Leyuan Li,Zhibin Ning,Xu Zhang,Janice Mayne,Kai Cheng,Alain Stintzi,Daniel Figeys,Daniel Figeys +7 more
TL;DR: An approach to screen compounds against individual microbiomes in vitro, using metaproteomics to both measure absolute bacterial abundances and to functionally profile the microbiome is developed, which enables multiple insights into microbiome absolute abundance and functional responses to drugs.
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PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data.
Rafael Hernández-de-Diego,Sonia Tarazona,Carlos Martínez-Mira,Leandro Balzano-Nogueira,Pedro Furió-Tarí,Georgios J. Pappas,Ana Conesa +6 more
TL;DR: PaintOmics 3 combines server-end capabilities for data analysis with the potential of modern web resources for data visualization, providing researchers with a powerful framework for interactive exploration of their multi-omics information.
Journal ArticleDOI
Altered Gut Microbiome Profile in Patients With Pulmonary Arterial Hypertension.
Seungbum Kim,Katya Rigatto,Marcelo Basso Gazzana,Marli Maria Knorst,Elaine M. Richards,Carl J. Pepine,Mohan K. Raizada +6 more
TL;DR: Patients with PAH exhibit a unique microbiome profile that has the high predictive potential for PAH, which highlights previously unknown roles of gut bacteria in this disease and could lead to new therapeutic, diagnostic, or management paradigms forPAH.
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