Investigation of the roles of trace elements during hepatitis C virus infection using protein-protein interactions and a shortest path algorithm

Zhu, Liucun; Chen, Xijia; Kong, Xiangyin; Cai, Yu-Dong

doi:10.1016/j.bbagen.2016.05.018

Cited by 10 publications

(7 citation statements)

References 140 publications

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“…1d , the average information centrality of 0.0004 for effector targets is significantly greater than that of non targets (0.0003; P < 0.0001). These data corroborate with previous findings in diverse host-pathogens systems including human- Burkholderia mallei network 44 , 45 . Collectively, our data suggest that Arabidopsis relies on effector targets to spread information through DEGs, and pathogen effectors may rewire the flow of information by interacting with these high value targets.…”

Section: Resultssupporting

confidence: 92%

“…1 ). Likewise, the shortest paths in combination with other centrality measures revealed novel genes, pathways, and microbial communities in other biological systems 44 , 45 , 65 – 67 . For instance, network topology analyses, i.e .…”

Section: Discussionmentioning

confidence: 96%

“…Similarly, network analysis in human- Burkholderia mallei recently showed that pathogen virulence factors interact with multifunctional host hub proteins to simultaneously manipulate a wide range of host cellular processes 65 . In another study, viral proteins also interact with key host proteins to hijack diverse signaling pathways for infectivity 44 , 45 . Shortest path centrality successfully identified human proteins targeted by hepatitis C virus as well as influenza A/H7N9 virus 44 , 45 .…”

Section: Discussionmentioning

confidence: 99%

“…In another study, viral proteins also interact with key host proteins to hijack diverse signaling pathways for infectivity 44 , 45 . Shortest path centrality successfully identified human proteins targeted by hepatitis C virus as well as influenza A/H7N9 virus 44 , 45 . Given that effector targets are highly connected proteins and pairs of immune interactors are closer to each other than non immune interactors in AI-1 MAIN 30 , 32 , 33 , we concluded that effector targets relay biological information using DEGs in Arabidopsis.…”

Section: Discussionmentioning

confidence: 99%

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Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity

Mishra

Sun

Ahmed

et al. 2017

Sci Rep

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The universal nature of networks’ structural and physical properties across diverse systems offers a better prospect to elucidate the interplay between a system and its environment. In the last decade, several large-scale transcriptome and interactome studies were conducted to understand the complex and dynamic nature of interactions between Arabidopsis and its bacterial pathogen, Pseudomonas syringae pv. tomato DC3000. We took advantage of these publicly available datasets and performed “-omics”-based integrative, and network topology analyses to decipher the transcriptional and protein-protein interaction activities of effector targets. We demonstrated that effector targets exhibit shorter distance to differentially expressed genes (DEGs) and possess increased information centrality. Intriguingly, effector targets are differentially expressed in a sequential manner and make for 1% of the total DEGs at any time point of infection with virulent or defense-inducing DC3000 strains. We revealed that DC3000 significantly alters the expression levels of 71% effector targets and their downstream physical interacting proteins in Arabidopsis interactome. Our integrative “-omics”-–based analyses identified dynamic complexes associated with MTI and disease susceptibility. Finally, we discovered five novel plant defense players using a systems biology-fueled top-to-bottom approach and demonstrated immune-related functions for them, further validating the power and resolution of our network analyses.

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Section: Resultssupporting

confidence: 92%

Section: Discussionmentioning

confidence: 96%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity

Mishra

Sun

Ahmed

et al. 2017

Sci Rep

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“…Zhu, X. Chen, X. Kong, and Y.D. Cai, [13] proposed a computational method to identify the genes related to the Hepatitis C Virus (HCV) and trace element metabolism factor. The searching process were involved in three steps, (1) applying shortest path in the PPI network, (2) excluded the un-related genes in the path, and (3) find the core genes related to the HCV and trace element metabolism factor.…”

Section: Literature Reviewmentioning

confidence: 99%

Identification of Lung Cancer Related Genes Using Enhanced Floyd Warshall Algorithm in a Protein to Protein Interaction Network

Patil¹,

Patil²,

Manickam³

2018

IJIES

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Lung cancer is defined as an uncontrolled cell growing in the tissues of lung, which is also said to be lung tumor. The lung cancer is curable in the starting stage, but identifying the lung cancer in starting stage is very difficult. In recent decades, researchers showed great interest on gene level lung cancer identification using shortest path between the lung cancer related genes. Many research has been done to identify the shortest path between the genes, but the conventional methods consumes more time for processing the data. In this research, Protein to Protein Interaction (PPI) structure is constructed from the weighted protein present in the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. For identifying the shortest path between the genes in PPI, an effective algorithm: enhanced Floyd warshall algorithm is proposed. Floyd warshall is efficient in finding the shortest path between the genes and also solves all pairs of shortest path problem. A major drawback of Floyd warshall algorithm is, it works slower than other conventional algorithms designed to perform the same task. To improve the performance of traditional Floyd warshall algorithm, an iterative matrix is used for eliminating the invalid path. Then, the comparison between the proposed method and existing system is given in the experimental result. Experimental outcome shows that the proposed approach improved the time consumption up to 2-3 sec compared to the existing methods: Dijkstra's algorithm and Floyd warshall algorithm.Keywords: Dijkstra's algorithm, Enhanced Floyd warshall algorithm, Protein to protein interaction, Search tool for the retrieval of interacting genes/proteins.

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Serum Zinc Deficiency and its Relation to Liver Fibrosis in Chronic HCV: a Real-Life Egyptian Study

Omran

Darweesh

Fouad

et al. 2017

Biol Trace Elem Res

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Zinc is essential for the activation of approximately 300 metallo-enzymes. Serum and hepatic zinc is decreased in chronic liver disease patients, and zinc depletion has been suggested to accelerate liver fibrosis. The study was designed to assess Zinc status in chronic HCV Egyptian patients and its relationship to fibrosis stage diagnosed by FibroScan. This was a cross-sectional study on 297 Egyptian patients with naïve chronic HCV. All patients underwent laboratory tests (including assessment of serum Zinc) and liver stiffness measurement (LSM) by Transient Elastography (FibroScan). The study included 170 (57.2%) females and 127 (42.8%) males with a mean age 52.4 ± 10.2 years. Most of the patients had zinc deficiency as the mean zinc level was 55.5 ± 30.7 μg/dl. The FibroScan scores showed that 97 patients had mild to moderate fibrosis (≤F2), while 200 patients had advanced to severe fibrosis (˃F2). Zinc level was significantly lower in patients with ˃F2 than those with ≤F2 (52 ± 30.7 vs 62.5 ± 29.7, p value: 0.005), as the zinc values decreased with the progression of liver fibrosis. Serum zinc level had a negative significant correlation with INR and negative significant correlation with FibroScan score but no correlation to bilirubin, ALT, AST, or albumin. Most of Egyptian chronic liver disease patients had zinc deficiency. Zinc level gets significantly lower with progression of fibrosis. Zinc supplementation is essential before and during antiviral therapy for HCV.

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Investigation of the roles of trace elements during hepatitis C virus infection using protein-protein interactions and a shortest path algorithm

Cited by 10 publications

References 140 publications

Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity

Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity

Identification of Lung Cancer Related Genes Using Enhanced Floyd Warshall Algorithm in a Protein to Protein Interaction Network

Serum Zinc Deficiency and its Relation to Liver Fibrosis in Chronic HCV: a Real-Life Egyptian Study

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