DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions

Karyala, Prashanthi; Metri, Rahul; Bathula, Christopher; Yelamanchi, Syam K.; Sahoo, Lipika; Arjunan, Selvam; Sastri, Narayan P.; Chandra, Nagasuma

doi:10.1371/journal.pntd.0004965

Cited by 25 publications

(12 citation statements)

References 55 publications

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“…For example, HCVpro is an HCV-specific database for human–HCV PPIs [13] . DenHunt and DenvInt are databases for PPIs between human and dengue virus [14] , [15] . ZikaBase is an integrated database for the ZIKV–human interactome map [16] .…”

Section: Introductionmentioning

confidence: 99%

Comprehensive characterization of human–virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs

Zhou

et al. 2022

Computational and Structural Biotechnology Journal

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Section: Introductionmentioning

confidence: 99%

Comprehensive characterization of human–virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs

Zhou

et al. 2022

Computational and Structural Biotechnology Journal

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“…The first one consists of PPI for species-specific databases encompassing only one specific viral species. It includes NCBI HIV-1 Human Interaction Database [ 30 ], HCVpro [ 31 ], DenHunt [ 32 ], DenvInt [ 33 ] and ZikaBase [ 34 ]. The second category on the other hand comprises of a wider range of virus species databases such as Viruses.STRING [ 35 ], VirusMentha [ 36 ], PHISTO [ 37 ], VirHostNet [ 38 ] and HPIDB [ 39 ].…”

Section: Introductionmentioning

confidence: 99%

Interactome of human and SARS-CoV-2 proteins to identify human hub proteins associated with comorbidities

Ghosh

Saha

Sharma

2021

Computers in Biology and Medicine

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SARS-CoV-2 has a higher chance of progression in adults of any age with certain underlying health conditions or comorbidities like cancer, neurological diseases and in certain cases may even lead to death. Like other viruses, SARS-CoV-2 also interacts with host proteins to pave its entry into host cells. Therefore, to understand the behaviour of SARS-CoV-2 and design of effective antiviral drugs, host-virus protein-protein interactions (PPIs) can be very useful. In this regard, we have initially created a human-SARS-CoV-2 PPI database from existing works in the literature which has resulted in 7085 unique PPIs. Subsequently, we have identified at most 10 proteins with highest degrees viz. hub proteins from interacting human proteins for individual virus protein. The identification of these hub proteins is important as they are connected to most of the other human proteins. Consequently, when they get affected, the potential diseases are triggered in the corresponding pathways, thereby leading to comorbidities. Furthermore, the biological significance of the identified hub proteins is shown using KEGG pathway and GO enrichment analysis. KEGG pathway analysis is also essential for identifying the pathways leading to comorbidities. Among others, SARS-CoV-2 proteins viz. NSP2, NSP5, Envelope and ORF10 interacting with human hub proteins like COX4I1, COX5A, COX5B, NDUFS1, CANX, HSP90AA1 and TP53 lead to comorbidities. Such comorbidities are Alzheimer, Parkinson, Huntington, HTLV-1 infection, prostate cancer and viral carcinogenesis. Subsequently, using Enrichr tool possible repurposable drugs which target the human hub proteins are reported in this paper as well. Therefore, this work provides a consolidated study for human-SARS-CoV-2 protein interactions to understand the relationship between comorbidity and hub proteins so that it may pave the way for the development of anti-viral drugs.

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“…An in silico study using DenHunt has shown that the dengue viral proteins are interacted directly with some proteins involved in Rap1 signaling pathway (Karyala et al, 2016). Those interactions are believed to interfere with the expression of host miRNA, resulting in a differential expression of some specific miRNAs.…”

Section: Discussionmentioning

confidence: 99%

MicroRNA profiling of mouse liver in response to DENV-1 infection by deep sequencing

Pong

Parkkinen

Dhanoa

et al. 2019

PeerJ

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Background Dengue caused by dengue virus (DENV) serotypes −1 to −4 is the most important mosquito-borne viral disease in the tropical and sub-tropical countries worldwide. Yet many of the pathophysiological mechanisms of host responses during DENV infection remain largely unknown and incompletely understood. Methods Using a mouse model, the miRNA expressions in liver during DENV-1 infection was investigated using high throughput miRNA sequencing. The differential expressions of miRNAs were then validated by qPCR, followed by target genes prediction. The identified miRNA targets were subjected to gene ontology (GO) annotation and pathway enrichment analysis to elucidate the potential biological pathways and molecular mechanisms associated with DENV-1 infection. Results A total of 224 and 372 miRNAs out of 433 known mouse miRNAs were detected in the livers of DENV-1-infected and uninfected mice, respectively; of these, 207 miRNAs were present in both libraries. The miR-148a-3p and miR-122-5p were the two most abundant miRNAs in both groups. Thirty-one miRNAs were found to have at least 2-fold change in upregulation or downregulation, in which seven miRNAs were upregulated and 24 miRNAs were downregulated in the DENV-1-infected mouse livers. The miR-1a-3p was found to be the most downregulated miRNA in the DENV-1-infected mouse livers, with a significant fold change of 0.10. To validate the miRNA sequencing result, the expression pattern of 12 miRNAs, which were highly differentially expressed or most abundant, were assessed by qPCR and nine of them correlated positively with the one observed in deep sequencing. In silico functional analysis revealed that the adaptive immune responses involving TGF-beta, MAPK, PI3K-Akt, Rap1, Wnt and Ras signalling pathways were modulated collectively by 23 highly differentially expressed miRNAs during DENV-1 infection. Conclusion This study provides the first insight into the global miRNA expressions of mouse livers in response to DENV-1 infection in vivo and the possible roles of miRNAs in modulating the adaptive immune responses during DENV-1 infection.

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DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions

Cited by 25 publications

References 55 publications

Comprehensive characterization of human–virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs

Comprehensive characterization of human–virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs

Interactome of human and SARS-CoV-2 proteins to identify human hub proteins associated with comorbidities

MicroRNA profiling of mouse liver in response to DENV-1 infection by deep sequencing

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