Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders

Nashiry, MA; Sumi, SS; Sharif Shohan, MU; Alyami, SA; Azad, AKM; Moni, MA

Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders

Nashiry, MA Sumi, SS Sharif Shohan, MU Alyami, SA Azad, AKM Moni, MA

Permalink

Publisher:: Oxford University Press (OUP)
Publication Type:: Journal Article
Citation:: Briefings in Bioinformatics, 2021, 22, (6)
Issue Date:: 2021-11-05

Closed Access

	Filename	Description	Size
	Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders.pdf	Published version	8.14 MB	Adobe PDF	View/Open

Copyright Clearance Process

Recently Added
In Progress
Closed Access

This item is closed access and not available.

Full metadata record

Field	Value	Language
dc.contributor.author	Nashiry, MA
dc.contributor.author	Sumi, SS
dc.contributor.author	Sharif Shohan, MU
dc.contributor.author	Alyami, SA
dc.contributor.author	Azad, AKM
dc.contributor.author	Moni, MA
dc.date.accessioned	2022-03-17T06:52:48Z
dc.date.available	2022-03-17T06:52:48Z
dc.date.issued	2021-11-05
dc.identifier.citation	Briefings in Bioinformatics, 2021, 22, (6)
dc.identifier.issn	1467-5463
dc.identifier.issn	1477-4054
dc.identifier.uri	http://hdl.handle.net/10453/155294
dc.description.abstract	<jats:title>Abstract</jats:title> <jats:p>Coronavirus Disease 2019 (COVID-19), although most commonly demonstrates respiratory symptoms, but there is a growing set of evidence reporting its correlation with the digestive tract and faeces. Interestingly, recent studies have shown the association of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection with gastrointestinal symptoms in infected patients but any sign of respiratory issues. Moreover, some studies have also shown that the presence of live SARS-CoV-2 virus in the faeces of patients with COVID-19. Therefore, the pathophysiology of digestive symptoms associated with COVID-19 has raised a critical need for comprehensive investigative efforts. To address this issue we have developed a bioinformatics pipeline involving a system biological framework to identify the effects of SARS-CoV-2 messenger RNA expression on deciphering its association with digestive symptoms in COVID-19 positive patients. Using two RNA-seq datasets derived from COVID-19 positive patients with celiac (CEL), Crohn’s (CRO) and ulcerative colitis (ULC) as digestive disorders, we have found a significant overlap between the sets of differentially expressed genes from SARS-CoV-2 exposed tissue and digestive tract disordered tissues, reporting 7, 22 and 13 such overlapping genes, respectively. Moreover, gene set enrichment analysis, comprehensive analyses of protein–protein interaction network, gene regulatory network, protein–chemical agent interaction network revealed some critical association between SARS-CoV-2 infection and the presence of digestive disorders. The infectome, diseasome and comorbidity analyses also discover the influences of the identified signature genes in other risk factors of SARS-CoV-2 infection to human health. We hope the findings from this pathogenetic analysis may reveal important insights in deciphering the complex interplay between COVID-19 and digestive disorders and underpins its significance in therapeutic development strategy to combat against COVID-19 pandemic.</jats:p>
dc.language	en
dc.publisher	Oxford University Press (OUP)
dc.relation.ispartof	Briefings in Bioinformatics
dc.relation.isbasedon	10.1093/bib/bbab126
dc.rights	info:eu-repo/semantics/closedAccess
dc.subject	0601 Biochemistry and Cell Biology, 0802 Computation Theory and Mathematics, 0899 Other Information and Computing Sciences
dc.subject.classification	Bioinformatics
dc.title	Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders
dc.type	Journal Article
utslib.citation.volume	22
utslib.for	0601 Biochemistry and Cell Biology
utslib.for	0802 Computation Theory and Mathematics
utslib.for	0899 Other Information and Computing Sciences
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
utslib.copyright.status	closed_access	*
dc.date.updated	2022-03-17T06:52:39Z
pubs.issue	6
pubs.publication-status	Published
pubs.volume	22
utslib.citation.issue	6

Abstract:

Abstract Coronavirus Disease 2019 (COVID-19), although most commonly demonstrates respiratory symptoms, but there is a growing set of evidence reporting its correlation with the digestive tract and faeces. Interestingly, recent studies have shown the association of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection with gastrointestinal symptoms in infected patients but any sign of respiratory issues. Moreover, some studies have also shown that the presence of live SARS-CoV-2 virus in the faeces of patients with COVID-19. Therefore, the pathophysiology of digestive symptoms associated with COVID-19 has raised a critical need for comprehensive investigative efforts. To address this issue we have developed a bioinformatics pipeline involving a system biological framework to identify the effects of SARS-CoV-2 messenger RNA expression on deciphering its association with digestive symptoms in COVID-19 positive patients. Using two RNA-seq datasets derived from COVID-19 positive patients with celiac (CEL), Crohn’s (CRO) and ulcerative colitis (ULC) as digestive disorders, we have found a significant overlap between the sets of differentially expressed genes from SARS-CoV-2 exposed tissue and digestive tract disordered tissues, reporting 7, 22 and 13 such overlapping genes, respectively. Moreover, gene set enrichment analysis, comprehensive analyses of protein–protein interaction network, gene regulatory network, protein–chemical agent interaction network revealed some critical association between SARS-CoV-2 infection and the presence of digestive disorders. The infectome, diseasome and comorbidity analyses also discover the influences of the identified signature genes in other risk factors of SARS-CoV-2 infection to human health. We hope the findings from this pathogenetic analysis may reveal important insights in deciphering the complex interplay between COVID-19 and digestive disorders and underpins its significance in therapeutic development strategy to combat against COVID-19 pandemic.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/155294