A Systems Bioinformatics Approach to Interconnect Biological Pathways

Minadakis, George

doi:10.1007/978-1-0716-0822-7_17

Cited by 3 publications

(1 citation statement)

References 31 publications

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“…Different biological pathways often interconnect spatially or temporally, triggered by a group of genes, proteins, and metabolites [ 83 ]. In E. coli , it is well known that flagellum production is associated with the virulence of EHEC O157:H7, and it has been shown that flagellum production varies among different infection stages, with flagella being produced at early stages for attachment of bacterial cells but not expressed in bacterial cells at later time points [ 63 ].…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Genomic island-encoded regulatory proteins in enterohemorrhagic Escherichia coli O157:H7

Wang,

Sun,

Kang

et al. 2024

Virulence

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Enterohemorrhagic Escherichia coli (EHEC) is an important zoonotic pathogen that is a major cause of foodborne diseases in most developed and developing countries and can cause uncomplicated diarrhoea, haemorrhagic colitis, and haemolytic uraemic syndrome. O islands (OIs), which are unique genomic islands in EHEC O157:H7, are composed of 177 isolated genomic features and harbour 26% of the total genes that are absent in the non-pathogenic E. coli K-12 genome. In the last twenty years, many OI-encoded proteins have been characterized, including proteins regulating virulence, motility, and acid resistance. Given the critical role of regulatory proteins in the systematic and hierarchical regulation of bacterial biological processes, this review summarizes the OI-encoded regulatory proteins in EHEC O157:H7 characterized to date, emphasizing OI-encoded regulatory proteins for bacterial virulence, motility, and acid resistance. This summary will be significant for further exploration and understanding of the virulence and pathogenesis of EHEC O157:H7.

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Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Genomic island-encoded regulatory proteins in enterohemorrhagic Escherichia coli O157:H7

Wang,

Sun,

Kang

et al. 2024

Virulence

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PathExNET: A tool for extracting pathway expression networks from gene expression statistics

Minadakis

Fuentes

Tsouloupas

et al. 2021

Computational and Structural Biotechnology Journal

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A fundamental issue related to the understanding of the molecular mechanisms, is the way in which common pathways act across different biological experiments related to complex diseases. Using network-based approaches, this work aims to provide a numeric characterization of pathways across different biological experiments, in the prospect to create unique footprints that may characterise a specific disease under study at a pathway network level. In this line we propose PathExNET, a web service that allows the creation of pathway-to-pathway expression networks that hold the over- and under expression information obtained from differential gene expression analyses. The unique numeric characterization of pathway expression status related to a specific biological experiment (or disease), as well as the creation of diverse combination of pathway networks generated by PathExNET, is expected to provide a concrete contribution towards the individualization of disease, and further lead to a more precise personalised medicine and management of treatment. PathExNET is available at: https://bioinformatics.cing.ac.cy/PathExNET and at https://pathexnet.cing-big.hpcf.cyi.ac.cy/

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PathIN: an integrated tool for the visualization of pathway interaction networks

Minadakis

Christodoulou

Tsouloupas

et al. 2023

Computational and Structural Biotechnology Journal

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A Systems Bioinformatics Approach to Interconnect Biological Pathways

Cited by 3 publications

References 31 publications

Genomic island-encoded regulatory proteins in enterohemorrhagic Escherichia coli O157:H7

Genomic island-encoded regulatory proteins in enterohemorrhagic Escherichia coli O157:H7

PathExNET: A tool for extracting pathway expression networks from gene expression statistics

PathIN: an integrated tool for the visualization of pathway interaction networks

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