Mechanistic modeling of the SARS-CoV-2 disease map
Open Access
- 21 January 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in BioData Mining
- Vol. 14 (1), 1-8
- https://doi.org/10.1186/s13040-021-00234-1
Abstract
Here we present a web interface that implements a comprehensive mechanistic model of the SARS-CoV-2 disease map. In this framework, the detailed activity of the human signaling circuits related to the viral infection, covering from the entry and replication mechanisms to the downstream consequences as inflammation and antigenic response, can be inferred from gene expression experiments. Moreover, the effect of potential interventions, such as knock-downs, or drug effects (currently the system models the effect of more than 8000 DrugBank drugs) can be studied. This freely available tool not only provides an unprecedentedly detailed view of the mechanisms of viral invasion and the consequences in the cell but has also the potential of becoming an invaluable asset in the search for efficient antiviral treatments.Keywords
Other Versions
Funding Information
- Ministerio de Economía y Competitividad (SAF2017-88908-R)
- Instituto de Salud Carlos III (PT17/0009/0006, COV20/00788, ACCI2018/29)
- FP7 People: Marie-Curie Actions (813533)
This publication has 36 references indexed in Scilit:
- Actionable pathways: interactive discovery of therapeutic targets using signaling pathway modelsNucleic Acids Research, 2016
- Translation of Genotype to Phenotype by a Hierarchy of Cell SubsystemsCell Systems, 2016
- Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesisMolecular Metabolism, 2016
- Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patientsScience Signaling, 2015
- Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivityScientific Reports, 2015
- KEGG as a reference resource for gene and protein annotationNucleic Acids Research, 2015
- Space and time: New considerations about the relationship between Toll-like receptors (TLRs) and type I interferons (IFNs)Cytokine, 2015
- Assessing the impact of mutations found in next generation sequencing data over human signaling pathwaysNucleic Acids Research, 2015
- Type I Interferon: A New Player in TNF SignalingPublished by S. Karger AG ,2010
- Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic DataPLoS Computational Biology, 2009