CEIT-OHSU
Reactome IDG Portal: Pathway-Based Analysis and Visualization of Understudied Human Proteins
https://reactome.org/
Guanming Wu, Ph.D.
Assistant Professor of Medical Informatics
Clinical Epidemiology School of Medicine
Biomedical Informatics Graduate Program School of Medicine
Oregon Health & Science University
Assistant Professor of Medical Informatics
Clinical Epidemiology School of Medicine
Biomedical Informatics Graduate Program School of Medicine
Oregon Health & Science University
Lincoln C. Stein, Ph.D.
Head
Adaptive Oncology
Ontario
Institute for Cancer Research
Head
Adaptive Oncology
Ontario
Institute for Cancer Research
Peter G. D’Eustachio, Ph.D.
Professor
Department of Biochemistry and Molecular Pharmacology
Professor, Department of Medicine
New York University Langone Health
Professor
Department of Biochemistry and Molecular Pharmacology
Professor, Department of Medicine
New York University Langone Health
Contacts
Lab websites:- Guanming Wu profile: https://www.ohsu.edu/people/guanming-wu/AFE03F1A939AA306550C5CE1128B9F36
- Lincoln C. Stein profile: https://oicr.on.ca/investigators/lincoln-stein/
- Peter G. D’Eustachio profile: https://med.nyu.edu/faculty/peter-g-d-eustachio
Reactome: @reactome
Overview
Collaborative work by Dr. Guanming Wu, Dr. Lincoln Stein, and Dr. Peter D’Eustachio focuses on utilizing the REACTOME knowledgebase, a biological pathway database, for illuminating interactions of IDG proteins with other proteins and biological entities. The aim is to develop a special Reactome IDG pathway portal allowing for evaluation of these understudied proteins via their localization, potential interactions, and developing testable predictions.
NIH grant number: 1U01 CA239069
Outcome: https://idg.reactome.org/
Publications:
- Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D'Eustachio P. The reactome pathway knowledgebase 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D687-D692. doi: 10.1093/nar/gkab1028. PMID: 34788843; PMCID: PMC8689983.
- Rothfels K, Milacic M, Matthews L, Haw R, Sevilla C, Gillespie M, Stephan R, Gong C, Ragueneau E, May B, Shamovsky V, Wright A, Weiser J, Beavers D, Conley P, Tiwari K, Jassal B, Griss J, Senff-Ribeiro A, Brunson T, Petryszak R, Hermjakob H, D'Eustachio P, Wu G, Stein L. Using the Reactome Database. Curr Protoc. 2023 Apr;3(4):e722. doi: 10.1002/cpz1.722. PMID: 37053306.
- Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, Haw R, Jassal B, Matthews L, May B, Petryszak R, Ragueneau E, Rothfels K, Sevilla C, Shamovsky V, Stephan R, Tiwari K, Varusai T, Weiser J, Wright A, Wu G, Stein L, Hermjakob H, D'Eustachio P. The Reactome Pathway Knowledgebase 2024. Nucleic Acids Res. 2024 Jan 5;52(D1):D672-D678. doi: 10.1093/nar/gkad1025. PMID: 37941124; PMCID: PMC10767911.
- Brunson T, Sanati N, Matthews L, Haw R, Beavers D, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D'Eustachio P, Wu G. Illuminating Dark Proteins using Reactome Pathways. bioRxiv [Preprint]. 2023 Jun 5:2023.06.05.543335. doi: 10.1101/2023.06.05.543335. PMID: 37333417; PMCID: PMC10274615.
- Tiwari K, Matthews L, May B, Shamovsky V, Orlic-Milacic M, Rothfels K, Ragueneau E, Gong C, Stephan R, Li N, Wu G, Stein L, D'Eustachio P, Hermjakob H. ChatGPT usage in the Reactome curation process. bioRxiv [Preprint]. 2023 Nov 8:2023.11.08.566195. doi: 10.1101/2023.11.08.566195. PMID: 37986970; PMCID: PMC10659344.
- Anderson AN, Conley P, Klocke CD, Sengupta SK, Pang A, Farley HC, Gillingham AR, Dawson AD, Fan Y, Jones JA, Gibbs SL, Skalet AH, Wu G, Wong MH. Detection of neoplastic-immune hybrid cells with metastatic properties in uveal melanoma. Res Sq [Preprint]. 2023 Dec 6:rs.3.rs-3694879. doi: 10.21203/rs.3.rs-3694879/v1. PMID: 38106024; PMCID: PMC10723549.
- Raimondi F, Burkhart JG, Betts MJ, Russell RB, Wu G. Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces. F1000Res. 2021 Nov 3;10:1111. doi: 10.12688/f1000research.74395.3. PMID: 36569594; PMCID: PMC9755755.
- Blucher AS, McWeeney SK, Stein L, Wu G. Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz. F1000Res. 2019 Jun 20;8:908. doi: 10.12688/f1000research.19592.1. PMID: 31372215; PMCID: PMC6644836.
- Beavers D, Brunson T, Sanati N, Matthews L, Haw R, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D'Eustachio P, Wu G. Illuminate the Functions of Dark Proteins Using the Reactome-IDG Web Portal. Curr Protoc. 2023 Jul;3(7):e845. doi: 10.1002/cpz1.845. PMID: 37467006; PMCID: PMC10399304.
- Brunson T, Sanati N, Huffman A, Masci AM, Zheng J, Cooke MF, Conley P, He Y, Wu G. VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data. Front Immunol. 2023 Mar 21;14:1141030. doi: 10.3389/fimmu.2023.1141030. PMID: 37180100; PMCID: PMC10172660.
- Klocke C, Moran A, Adey A, McWeeney S, Wu G. Identification of Cellular Interactions in the Tumor Immune Microenvironment Underlying CD8 T Cell Exhaustion. bioRxiv [Preprint]. 2023 Nov 13:2023.11.09.566384. doi: 10.1101/2023.11.09.566384. PMID: 38014233; PMCID: PMC10680664.