CoV-Hipathia
CoV-Hipathia models human signaling pathway activity and simulates drug and mutation effects to interpret molecular mechanisms of SARS-CoV-2 infection.
Key Features:
- Mechanistic modeling: Implements mechanistic models of signaling circuits involved in SARS-CoV-2 infection, including pathways related to viral entry, replication, inflammation, and antigenic response.
- Gene expression inference: Infers human signaling activity from gene expression data to assess how expression changes impact cellular responses during infection.
- Genomic mutation analysis: Interprets the impact of genomic mutations on signaling pathways and cellular mechanisms relevant to SARS-CoV-2.
- Intervention simulation: Simulates interventions such as gene knock-downs and drug effects, modeling over 8,000 drugs from DrugBank.
- Graph-based analysis: Provides graph-based disease modeling by integrating curated pathway diagrams with interaction and text-mining databases as part of the COVID-19 Disease Map (C19DMap) initiative.
- C19DMap integration: Leverages the curated dataset and computable repository from the COVID-19 Disease Map project for pathway and mechanism interpretation.
Scientific Applications:
- Antiviral candidate discovery: Supports identification and prioritization of potential antiviral drugs by simulating drug effects on signaling pathways.
- Therapeutic target identification: Aids identification of molecular targets by revealing pathway nodes and circuits altered by infection or mutation.
- Biomarker and signature discovery: Enables detection of gene expression and mutation signatures related to SARS-CoV-2 predisposition and treatment response.
- Hypothesis generation on virus-host interactions: Facilitates proposal of testable hypotheses about mechanisms of SARS-CoV-2 invasion and host cellular consequences via graph-based analyses.
Methodology:
Integrates curated knowledge from the COVID-19 Disease Map (C19DMap) and literature by curating pathway diagrams and linking them with interaction and text-mining databases; infers signaling activity from gene expression and genomic mutation data; performs graph-based analyses and simulates interventions including gene knock-downs and DrugBank drug effects.
Topics
Collections
Details
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- web application
- Operating Systems:
- Mac, Linux, Windows
- Programming Languages:
- JavaScript, R, SQL
- Added:
- 3/11/2022
- Last Updated:
- 3/14/2022
Operations
Publications
Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-Chilet M, Dopazo J. Mechanistic modeling of the SARS-CoV-2 disease map. BioData Mining. 2021;14(1). doi:10.1186/s13040-021-00234-1. PMID:33478554. PMCID:PMC7817765.
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta‐Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic‐Milacic M, Senff-Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban‐Medina M, Peña‐Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Willighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez‐Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms. Molecular Systems Biology. 2021;17(10). doi:10.15252/msb.202110387. PMID:34664389. PMCID:PMC8524328.
Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data. 2020;7(1). doi:10.1038/s41597-020-0477-8. PMID:32371892. PMCID:PMC7200764.