Building Protein-Protein Interaction Graph Database Using Neo4j

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2023 Jul 14

PMID 37450167

Authors

Nilesh Kumar

Shahid Mukhtar

Affiliations

Soon will be listed here.

Abstract

A cell's various components interact with each other in a coordinated manner to respond to environmental cues and intracellular signals. Compared to the other biological networks, the protein-protein interaction (PPI) is mostly responsible for maintaining signaling pathways. Increasing numbers of experimentally verified and predicted PPIs in plants demand a scalable platform to deal with large and complex datasets. Network/graph data can be organized and analyzed using different tools. This chapter uses Neo4j, a graph database management system, to store and analyze plant PPI networks. To make the graph database and analyze network centrality, we used Arabidopsis interactome-1 main (AI-1) PPI network.

Citing Articles

Integrated Systems Biology Pipeline to Compare Co-Expression Networks in Plants and Elucidate Differential Regulators.

Kumar N, Mukhtar M Plants (Basel). 2023; 12(20).

PMID: 37896081 PMC: 10610404. DOI: 10.3390/plants12203618.

References

Walport L, Low J, Matthews J, Mackay J . The characterization of protein interactions - what, how and how much?. Chem Soc Rev. 2021; 50(22):12292-12307. DOI: 10.1039/d1cs00548k. View

Wessling R, Epple P, Altmann S, He Y, Yang L, Henz S . Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Cell Host Microbe. 2014; 16(3):364-75. PMC: 4191710. DOI: 10.1016/j.chom.2014.08.004. View

Smakowska-Luzan E, Mott G, Parys K, Stegmann M, Howton T, Layeghifard M . An extracellular network of Arabidopsis leucine-rich repeat receptor kinases. Nature. 2018; 553(7688):342-346. PMC: 6485605. DOI: 10.1038/nature25184. View

Mukhtar M, Carvunis A, Dreze M, Epple P, Steinbrenner J, Moore J . Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science. 2011; 333(6042):596-601. PMC: 3170753. DOI: 10.1126/science.1203659. View

Mott G, Smakowska-Luzan E, Pasha A, Parys K, Howton T, Neuhold J . Map of physical interactions between extracellular domains of Arabidopsis leucine-rich repeat receptor kinases. Sci Data. 2019; 6:190025. PMC: 6390701. DOI: 10.1038/sdata.2019.25. View

Mishra B, Sun Y, Howton T, Kumar N, Mukhtar M . Dynamic modeling of transcriptional gene regulatory network uncovers distinct pathways during the onset of Arabidopsis leaf senescence. NPJ Syst Biol Appl. 2018; 4:35. PMC: 6119185. DOI: 10.1038/s41540-018-0071-2. View

Mishra B, Sun Y, Ahmed H, Liu X, Mukhtar M . Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity. Sci Rep. 2017; 7(1):7849. PMC: 5552879. DOI: 10.1038/s41598-017-08073-z. View

Mishra B, Kumar N, Mukhtar M . A rice protein interaction network reveals high centrality nodes and candidate pathogen effector targets. Comput Struct Biotechnol J. 2022; 20:2001-2012. PMC: 9062363. DOI: 10.1016/j.csbj.2022.04.027. View

Mishra B, Kumar N, Mukhtar M . Network biology to uncover functional and structural properties of the plant immune system. Curr Opin Plant Biol. 2021; 62:102057. DOI: 10.1016/j.pbi.2021.102057. View

10.

Mishra B, Kumar N, Mukhtar M . Systems Biology and Machine Learning in Plant-Pathogen Interactions. Mol Plant Microbe Interact. 2018; 32(1):45-55. DOI: 10.1094/MPMI-08-18-0221-FI. View

11.

Lopez J, Mukhtar M . Mapping Protein-Protein Interaction Using High-Throughput Yeast 2-Hybrid. Methods Mol Biol. 2017; 1610:217-230. DOI: 10.1007/978-1-4939-7003-2_14. View

12.

Kumar N, Mishra B, Mukhtar M . A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions. STAR Protoc. 2022; 3(3):101608. PMC: 9386103. DOI: 10.1016/j.xpro.2022.101608. View

13.

Kumar N, Mishra B, Mehmood A, Athar M, Mukhtar M . Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis. iScience. 2020; 23(9):101526. PMC: 7468341. DOI: 10.1016/j.isci.2020.101526. View

14.

Klopffleisch K, Phan N, Augustin K, Bayne R, Booker K, Botella J . Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Mol Syst Biol. 2011; 7:532. PMC: 3202803. DOI: 10.1038/msb.2011.66. View

15.

Gonzalez-Fuente M, Carrere S, Monachello D, Marsella B, Cazale A, Zischek C . EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome. Mol Plant Pathol. 2020; 21(10):1257-1270. PMC: 7488465. DOI: 10.1111/mpp.12965. View

16.

Garbutt C, Bangalore P, Kannar P, Mukhtar M . Getting to the edge: protein dynamical networks as a new frontier in plant-microbe interactions. Front Plant Sci. 2014; 5:312. PMC: 4074768. DOI: 10.3389/fpls.2014.00312. View

17.

Ahmed H, Howton T, Sun Y, Weinberger N, Belkhadir Y, Mukhtar M . Network biology discovers pathogen contact points in host protein-protein interactomes. Nat Commun. 2018; 9(1):2312. PMC: 5998135. DOI: 10.1038/s41467-018-04632-8. View

18.

Liu X, Salokas K, Weldatsadik R, Gawriyski L, Varjosalo M . Combined proximity labeling and affinity purification-mass spectrometry workflow for mapping and visualizing protein interaction networks. Nat Protoc. 2020; 15(10):3182-3211. DOI: 10.1038/s41596-020-0365-x. View

19.

Zahiri J, Yaghoubi O, Mohammad-Noori M, Ebrahimpour R, Masoudi-Nejad A . PPIevo: protein-protein interaction prediction from PSSM based evolutionary information. Genomics. 2013; 102(4):237-42. DOI: 10.1016/j.ygeno.2013.05.006. View

20.

Singh R, Park D, Xu J, Hosur R, Berger B . Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Res. 2010; 38(Web Server issue):W508-15. PMC: 2896152. DOI: 10.1093/nar/gkq481. View