PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways DOI Creative Commons
Julian Müller, Florian Bayer, Mathias Wilhelm

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 8, 2025

Abstract Post-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how modulate pathways on molecular level. Here, we present PTMNavigator, tool integrated into ProteomicsDB platform that offers an interactive interface researchers overlay experimental PTM data with pathway diagrams. PTMNavigator provides ~3000 canonical manually curated databases, enabling users modify create custom diagrams tailored data. Additionally, automatically runs kinase enrichment algorithms whose results are directly visualization. This view intricate relationship between signaling pathways. We demonstrate utility by applying it two phosphoproteomics datasets, showing can enhance analysis, visualize drug treatments result discernable flow PTM-driven aid proposing extensions existing By enhancing understanding dynamics facilitating discovery PTM-pathway interactions, advances knowledge biology its implications health disease.

Language: Английский

The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information DOI Creative Commons
John H. Morris, Karthik Soman, Rabia E Akbas

et al.

Bioinformatics, Journal Year: 2023, Volume and Issue: 39(2)

Published: Feb. 1, 2023

Abstract Motivation Knowledge graphs (KGs) are being adopted in industry, commerce and academia. Biomedical KG presents a challenge due to the complexity, size heterogeneity of underlying information. Results In this work, we present Scalable Precision Medicine Open Engine (SPOKE), biomedical connecting millions concepts via semantically meaningful relationships. SPOKE contains 27 million nodes 21 different types 53 edges 55 downloaded from 41 databases. The graph is built on framework 11 ontologies that maintain its structure, enable mappings facilitate navigation. weekly by python scripts which download each resource, check for integrity completeness, then create ‘parent table’ edges. Graph queries translated REST API users can submit searches directly an or graphical user interface. Conclusions/Significance: enables integration seemingly disparate information support precision medicine efforts. Availability implementation neighborhood explorer available at https://spoke.rbvi.ucsf.edu. Supplementary data Bioinformatics online.

Language: Английский

Citations

44
Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review DOI Creative Commons
Diletta Rosati, Maria Palmieri,

Giulia Brunelli

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 1154 - 1168

Published: March 1, 2024

In recent years, the role of bioinformatics and computational biology together with omics techniques transcriptomics has gained tremendous importance in biomedicine healthcare, particularly for identification biomarkers precision medicine drug discovery. Differential gene expression (DGE) analysis is one most used RNA-sequencing (RNA-seq) data analysis. This tool, which typically various RNA-seq processing applications, allows differentially expressed genes across two or more sample sets. Functional enrichment analyses can then be performed to annotate contextualize resulting lists. These studies provide valuable information about disease-causing biological processes help identifying molecular targets novel therapies. review focuses on differential pipelines commonly identify specific discuss advantages disadvantages these techniques.

Language: Английский

Citations

33
Sepsis-trained macrophages promote antitumoral tissue-resident T cells DOI

Alexis Broquet,

Victor Gourain, Thomas Goronflot

et al.

Nature Immunology, Journal Year: 2024, Volume and Issue: 25(5), P. 802 - 819

Published: April 29, 2024

Language: Английский

Citations

19
Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing DOI Creative Commons
Andreas Maier, Michael Hartung,

Mark Abovsky

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(W1), P. W481 - W488

Published: May 23, 2024

Abstract In recent decades, the development of new drugs has become increasingly expensive and inefficient, molecular mechanisms most pharmaceuticals remain poorly understood. response, computational systems network medicine tools have emerged to identify potential drug repurposing candidates. However, these often require complex installation lack intuitive visual mining capabilities. To tackle challenges, we introduce Drugst.One, a platform that assists specialized in becoming user-friendly, web-based utilities for repurposing. With just three lines code, Drugst.One turns any biology software into an interactive web tool modeling analyzing protein-drug-disease networks. Demonstrating its broad adaptability, been successfully integrated with 21 tools. Available at https://drugst.one, significant streamlining discovery process, allowing researchers focus on essential aspects pharmaceutical treatment research.

Language: Английский

Citations

17
PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways DOI Creative Commons
Julian Müller, Florian Bayer, Mathias Wilhelm

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 8, 2025

Abstract Post-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how modulate pathways on molecular level. Here, we present PTMNavigator, tool integrated into ProteomicsDB platform that offers an interactive interface researchers overlay experimental PTM data with pathway diagrams. PTMNavigator provides ~3000 canonical manually curated databases, enabling users modify create custom diagrams tailored data. Additionally, automatically runs kinase enrichment algorithms whose results are directly visualization. This view intricate relationship between signaling pathways. We demonstrate utility by applying it two phosphoproteomics datasets, showing can enhance analysis, visualize drug treatments result discernable flow PTM-driven aid proposing extensions existing By enhancing understanding dynamics facilitating discovery PTM-pathway interactions, advances knowledge biology its implications health disease.

Language: Английский

Citations

2