A Graph-Based Approach for Finding the Dengue Infection Pathways in Humans Using Protein–Protein Interactions

Dey, Lopamudra; Mukhopadhyay, Anirban

doi:10.1089/cmb.2019.0171

Cited by 7 publications

(7 citation statements)

References 27 publications

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“…We have to underline that YFV repertoires are missing in two of our MS databases, this may impact significance. Interestingly, in a Taiwan cohort of MS patients, DENV has been associated with autoimmune and neurological diseases [41] and DENV infections have been suggested to lead to various diseases in humans [42]. On the other hand, finding sequences associated with CD is in agreement with the idea that MS shares the genetic basis with other complex diseases (e.g., rheumatoid arthritis, diabetes, CD), involving coincidence of variants involved in the immune response [43,44].…”

Section: Discussionmentioning

confidence: 78%

TCR repertoire diversity in Multiple Sclerosis: High-dimensional bioinformatics analysis of sequences from brain, cerebrospinal fluid and peripheral blood

Amoriello¹,

Chernigovskaya²,

Greiff³

et al. 2021

EBioMedicine

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Background: T cells play a key role in the pathogenesis of multiple sclerosis (MS), a chronic, inflammatory, demyelinating disease of the central nervous system (CNS). Although several studies recently investigated the T-cell receptor (TCR) repertoire in cerebrospinal fluid (CSF) of MS patients by high-throughput sequencing (HTS), a deep analysis on repertoire similarities and differences among compartments is still missing. Methods: We performed comprehensive bioinformatics on high-dimensional TCR Vb sequencing data from published and unpublished MS and healthy donors (HD) studies. We evaluated repertoire polarization, clone distribution, shared CDR3 amino acid sequences (CDR3s-a.a.) across repertoires, clone overlap with public databases, and TCR similarity architecture. Findings: CSF repertoires showed a significantly higher public clones percentage and sequence similarity compared to peripheral blood (PB). On the other hand, we failed to reject the null hypothesis that the repertoire polarization is the same between CSF and PB. One Primary-Progressive MS (PPMS) CSF repertoire differed from the others in terms of TCR similarity architecture. Cluster analysis splits MS from HD. Interpretation: In MS patients, the presence of a physiological barrier, the blood-brain barrier, does not impact clone prevalence and distribution, but impacts public clones, indicating CSF as a more private site. We reported a high Vb sequence similarity in the CSF-TCR architecture in one PPMS. If confirmed it may be an interesting insight into MS progressive inflammatory mechanisms. The clustering of MS repertoires from HD suggests that disease shapes the TCR Vb clonal profile. Funding: This study was partly financially supported by the Italian Multiple Sclerosis Foundation (FISM), that contributed to Ballerini-DB data collection (grant #2015 R02).

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Section: Discussionmentioning

confidence: 78%

TCR repertoire diversity in Multiple Sclerosis: High-dimensional bioinformatics analysis of sequences from brain, cerebrospinal fluid and peripheral blood

Amoriello¹,

Chernigovskaya²,

Greiff³

et al. 2021

EBioMedicine

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“…Dengue, covid and Zika viruses have 15, 3 and 3 interacting human proteins in common with Chikv respectively. For Dengue, they are GRN, CALCOCO2, HNRNPK, WWP1, XPO1, ACTG1, TSG101, COMMD1, DYNC1H1, G3BP2, EIF2A, PSAP, EEF1A1, TUBA1A, NAP1L1 (Dey and Mukhopadhyay 2017, 2020). For Covid FBLN5, SEPSECS, G3BP2 (Dey et al .…”

Section: Resultsmentioning

confidence: 99%

“…For Dengue, they are GRN, CALCOCO2, HNRNPK, WWP1, XPO1, ACTG1, TSG101, COMMD1, DYNC1H1, G3BP2, EIF2A, PSAP, EEF1A1, TUBA1A, NAP1L1 Mukhopadhyay 2017, 2020). For Covid FBLN5, SEP-SECS, G3BP2 (Dey et al 2020;Gordon et al 2020) and for Zika FBLN5, ATP1B, MAP1B (Golubeva et al 2020). We can see a larger overlapping of interacting proteins with Dengue which is also dominant in high-humidity regions like river basins.…”

Section: Overlapping Interactions With Other Virusesmentioning

confidence: 90%

ChikvInt: a Chikungunya virus–host protein–protein interaction database

Kusari

Dey²,

Mukhopadhyay

2022

Letters Applied Microbiology

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Significance and Impact of the Study: We develop a virus-host protein-protein interaction database and the corresponding public web server named ChikvInt. Chikungunya virus is a major threat to the tropical countries. No standard structured database is available to catalogue the protein-protein interactions between Chikungunya and host proteins. In this work, we have developed such a database through literature curation and made it public through a web server. We believe that this database will help the researchers identify effective drug targets to control its rapid spread inside the host body.

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“…Please ignore the colour differences in this example. Clearly, all maximal bicliques involving 2 and 3 are contained in Figures 3(a For instance, given the bidegeneracy order of the graph in Figure 1(a), BDorder= (1,7,2,6,11,12,8,3,4,5,9,10), vertices 3 and 4 centred subgraphs are black and red parts of Figures 3(a) and (b) respectively. A search order for tightening search space.…”

Section: From Sparse To Densementioning

confidence: 99%

“…Furthermore, it plays principal roles for analyzing biological data since an MBB is an important instance of bicluster [7,28]. Recently, it also draws significant attention for discovering interactions between proteins [4,19,12,14].…”

Section: Introductionmentioning

confidence: 99%

Efficient Exact Algorithms for Maximum Balanced Biclique Search in Bipartite Graphs

Chen

Liu

Zhou

et al. 2020

Preprint

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Given a bipartite graph, the maximum balanced biclique (MBB) problem, discovering a mutually connected while equal-sized disjoint sets with the maximum cardinality, plays a significant role for mining the bipartite graph and has numerous applications. Despite the NP-hardness of the MBB problem, in this paper, we show that an exact MBB can be discovered extremely fast in bipartite graphs for real applications. We propose two exact algorithms dedicated for dense and sparse bipartite graphs respectively. For dense bipartite graphs, an O * (1.3803 n ) algorithm is proposed. This

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A Graph-Based Approach for Finding the Dengue Infection Pathways in Humans Using Protein–Protein Interactions

Cited by 7 publications

References 27 publications

TCR repertoire diversity in Multiple Sclerosis: High-dimensional bioinformatics analysis of sequences from brain, cerebrospinal fluid and peripheral blood

TCR repertoire diversity in Multiple Sclerosis: High-dimensional bioinformatics analysis of sequences from brain, cerebrospinal fluid and peripheral blood

ChikvInt: a Chikungunya virus–host protein–protein interaction database

Efficient Exact Algorithms for Maximum Balanced Biclique Search in Bipartite Graphs

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