Capturing context-specific regulation in molecular interaction networks

Rush, Stephen; Repsilber, Dirk

doi:10.1101/254730

Cited by 4 publications

(3 citation statements)

References 28 publications

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“…In the last decade, several methodologies have been developed to define and identify core regulatory networks, disease modules or context-specific subnetworks from large molecular interaction network ( Khan et al, 2018 ; Park et al, 2019 ; Rush and Repsilber, 2018 ; Dreyer et al, 2018 , Jaitly et al, 2020 , Saelens et al, 2018 , Singh et al, 2020 ). The AIR allows interfacing with such approaches in general through additional plugins.…”

Section: Discussionmentioning

confidence: 99%

The Atlas of Inflammation Resolution (AIR)

Serhan

Gupta

Perretti

et al. 2020

Molecular Aspects of Medicine

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129

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Acute inflammation is a protective reaction by the immune system in response to invading pathogens or tissue damage. Ideally, the response should be localized, self-limited, and returning to homeostasis. If not resolved, acute inflammation can result in organ pathologies leading to chronic inflammatory phenotypes. Acute inflammation and inflammation resolution are complex coordinated processes, involving a number of cell types, interacting in space and time. The biomolecular complexity and the fact that several biomedical fields are involved, make a multi- and interdisciplinary approach necessary. The Atlas of Inflammation Resolution (AIR) is a web-based resource capturing an essential part of the state-of-the-art in acute inflammation and inflammation resolution research. The AIR provides an interface for users to search thousands of interactions, arranged in inter-connected multi-layers of process diagrams, covering a wide range of clinically relevant phenotypes. By mapping experimental data onto the AIR, it can be used to elucidate drug action as well as molecular mechanisms underlying different disease phenotypes. For the visualization and exploration of information, the AIR uses the Minerva platform, which is a well-established tool for the presentation of disease maps. The molecular details of the AIR are encoded using international standards. The AIR was created as a freely accessible resource, supporting research and education in the fields of acute inflammation and inflammation resolution. The AIR connects research communities, facilitates clinical decision making, and supports research scientists in the formulation and validation of hypotheses. The AIR is accessible through https://air.bio.informatik.uni-rostock.de

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Section: Discussionmentioning

confidence: 99%

The Atlas of Inflammation Resolution (AIR)

Serhan

Gupta

Perretti

et al. 2020

Molecular Aspects of Medicine

Self Cite

129

View full text Add to dashboard Cite

show abstract

“…In the last decade, several methodologies have been developed to define and identify core regulatory network, disease modules, context-specific subnetworks from large molecular interaction network [44][45][46][47] . The AIR allows interfacing with such approaches in general through additional plugins.…”

Section: The Identification Of Core Regulatory Processesmentioning

confidence: 99%

The Atlas of Inflammation-Resolution (AIR)

Serhan

Gupta

Perretti

et al. 2020

Preprint

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Acute inflammation is a protective reaction by the immune system in response to invading pathogens or tissue damage. Ideally, the response should be localized, self-limited, and returning to homeostasis. If not resolved, acute inflammation can result in organ pathologies leading to chronic inflammatory phenotypes. Acute inflammation and inflammation resolution are complex coordinated processes, involving a number of cell types, interacting in space and time. The biomolecular complexity and the fact that several biomedical fields are involved, make a multi and interdisciplinary approach necessary. This Atlas of Inflammation Resolution (AIR) is a web-based resource capturing the state-of-theart in acute inflammation and inflammation resolution research. The AIR provides an interface for users to search thousands of interactions, arranged in inter-connected multi-layers of process diagrams, covering a wide range of clinically relevant phenotypes. The AIR serves as an open access knowledgebase, including a gateway to numerous public databases. It is furthermore possible for the user to map experimental data onto the molecular interaction maps of the AIR, providing the basis for bioinformatics analyses and systems biology approaches. By mapping experimental data onto the Atlas, it can be used to elucidate drug action as well as molecular mechanisms underlying different disease phenotypes. For the visualization and exploration of information, the AIR uses the Minerva platform, which is a well-established tool for the presentation of disease maps. The molecular details of the AIR are encoded using international standards.The Atlas of Inflammation Resolution was created as a freely accessible resource, supporting research and education in the fields of acute inflammation and inflammation resolution. The AIR connects research communities, facilitates clinical decision making, and supports research scientists in the formulation and validation of hypotheses. Abbreviations:

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“…Network-based algorithms predict drug or disease targets by combining network information and transcriptomic data [14, 21-27]. Two recent representatives, DeMAND [22] and ProTINA [14], model the systemic dysregulation of regulatory network caused by a drug treatment, connecting molecular interactions with differential expression (DE).…”

Section: Introductionmentioning

confidence: 99%