Comparative Study of Gene Expression Profiling Unravels Functions Associated with Pathogenesis of Dengue Infection

Warsi, Mohiuddin Khan; Kamal, Mohammad Azhar; Baeshen, Mohammed N.; Izhari, Mohammad Asrar; Firoz, Ahmad; Mobashir, Mohammad

doi:10.2174/1381612826666201106093148

Cited by 14 publications

(13 citation statements)

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“…In the previous work, we have exclusively explored (Warsi et al 2020), but more works have focused on gene expression profiling after DENV infection while different from these works (Ubol et al, 2008;Nascimento et al, 2009;Rothman, 2011;Sun et al, 2013;Datan et al, 2016;Sim and Hibberd, 2016;Simon-Lorière et al, 2017), we have compared the two datasets in terms of expression patterns and the altered functions. We were interested in learning more about the potential connection between DENV and SP infection in humans since the majority of infectious diseases are linked to the immune system, and our aim was to learn more about the infection's effect on the immune system.…”

Section: Discussionmentioning

confidence: 99%

Gene Expression Profiling of Early Acute Febrile Stage of Dengue Infection and Its Comparative Analysis With Streptococcus pneumoniae Infection

Bajrai

Sohrab

Alandijany

et al. 2021

Front. Cell. Infect. Microbiol.

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Infectious diseases are the disorders caused by organisms such as bacteria, viruses, fungi, or parasites. Although many of them are permentantly hazardous, a number of them live in and on our bodies and they are normally harmless or even helpful. Under certain circumstances, some organisms may cause diseases and these infectious diseases may be passed directly from person to person or via intermediate vectors including insects and other animals. Dengue virus and Streptococcus pneumoniae are the critical and common sources of infectious diseases. So, it is critical to understand the gene expression profiling and their inferred functions in comparison to the normal and virus infected conditions. Here, we have analyzed the gene expression profiling for dengue hemorrhagic fever, dengue fever, and normal human dataset. Similar to it, streptococcus pneumoniae infectious data were analyzed and both the outcomes were compared. Our study leads to the conclusion that the dengue hemorrhagic fever arises in result to potential change in the gene expression pattern, and the inferred functions obviously belong to the immune system, but also there are some additional potential pathways which are critical signaling pathways. In the case of pneumoniae infection, 19 pathways were enriched, almost all these pathways are associated with the immune system and 17 of the enriched pathways were common with dengue infection except platelet activation and antigen processing and presentation. In terms of the comparative study between dengue virus and Streptococcus pneumoniae infection, we conclude that cell adhesion molecules (CAMs), MAPK signaling pathway, natural killer cell mediated cytotoxicity, regulation of actin cytoskeleton, and cytokine-cytokine receptor interaction are commonly enriched in all the three cases of dengue infection and Streptococcus pneumoniae infection, focal adhesion was enriched between classical dengue fever — dengue hemorrhagic fever, dengue hemorrhagic fever—normal samples, and SP, and antigen processing and presentation and Leukocyte transendothelial migration were enriched in classical dengue fever —normal samples, dengue hemorrhagic fever—normal samples, and Streptococcus pneumoniae infection.

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Section: Discussionmentioning

confidence: 99%

Gene Expression Profiling of Early Acute Febrile Stage of Dengue Infection and Its Comparative Analysis With Streptococcus pneumoniae Infection

Bajrai

Sohrab

Alandijany

et al. 2021

Front. Cell. Infect. Microbiol.

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“…The list of DEGs has been processed for pathway enrichment analysis and understanding (56,57). The KEGG (37) database has been used for calculating enriched pathways, and our own code has been used for pathway and network analysis (58)(59)(60)(61).…”

Section: Methodsmentioning

confidence: 99%

In-Silico Study of Immune System Associated Genes in Case of Type-2 Diabetes With Insulin Action and Resistance, and/or Obesity

et al. 2021

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Type-2 diabetes and obesity are among the leading human diseases and highly complex in terms of diagnostic and therapeutic approaches and are among the most frequent and highly complex and heterogeneous in nature. Based on epidemiological evidence, it is known that the patients suffering from obesity are considered to be at a significantly higher risk of type-2 diabetes. There are several pieces of evidence that support the hypothesis that these diseases interlinked and obesity may aggravate the risk(s) of type-2 diabetes. Multi-level unwanted alterations such as (epi-) genetic alterations, changes at the transcriptional level, and altered signaling pathways (receptor, cytoplasmic, and nuclear level) are the major sources that promote several complex diseases, and such a heterogeneous level of complexity is considered as a major barrier in the development of therapeutics. With so many known challenges, it is critical to understand the relationships and the shared causes between type-2 diabetes and obesity, and these are difficult to unravel and understand. For this purpose, we have selected publicly available datasets of gene expression for obesity and type-2 diabetes, have unraveled the genes and the pathways associated with the immune system, and have also focused on the T-cell signaling pathway and its components. We have applied a simplified computational approach to understanding differential gene expression and patterns and the enriched pathways for obesity and type-2 diabetes. Furthermore, we have also analyzed genes by using network-level understanding. In the analysis, we observe that there are fewer genes that are commonly differentially expressed while a comparatively higher number of pathways are shared between them. There are only 4 pathways that are associated with the immune system in case of obesity and 10 immune-associated pathways in case of type-2 diabetes, and, among them, only 2 pathways are commonly altered. Furthermore, we have presented SPNS1, PTPN6, CD247, FOS, and PIK3R5 as the overexpressed genes, which are the direct components of TCR signaling.

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“…Furthermore, for the top 100 clinically signi cant genes, panther database 52 has been used for the panther protein classi cation. In short we could also say that the individual les have been prepared by using the command line codes (unix) for genes and pathways list preparations based on the relevant needs for the purpose to analyze the enriched pathways or preparing the networks or for panther protein class prediction [53][54][55] . 3.…”

Section: Methodsmentioning

confidence: 99%

Study of APOBEC3B focused breast cancer pathways and the clinical relevance

Choudhary¹,

Albukhari²,

Mobashir³

et al. 2021

Preprint

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APOBEC3B is considered as an enzymatic source of mutation in case of breast cancer and Human T-Cell Leukemia Virus Type 1 and Bone Leiomyosarcoma are also associated with it. The major functions controlled or affected due to APOBEC3B are gene expression, mRNA editing such as C -> U conversion, and deoxycytidine deaminase activity. Here, the main goal of the study was to perform a systematic analysis of APOBEC3B associated genes and its functional impact in human breast cancer. For this purpose, the datasets have been utilized from the publicly available database such as GEO, OncoLnc, and TCGA. Based on the requirements for fetching the values, different bioinformatics approaches have been applied at different levels. Further, co-regulated genes obtained from co-expression network have been processed and the mutated genes with the pathways enrichment analysis, and the clinical relevance using survival curve analysis by using OncoLnc have been performed. In the results, we found that there are a number of critical pathways known to directly associated with breast cancer are altered because of the genes which are either overexpressed or top mutated and are associated with APOBEC3B and these pathways are cell cycle, p53 signaling, immune signaling pathways, progesterone-mediated oocyte maturation, apoptosis, critical metabolic pathways, and pathways in cancers. From the mutational and survival analysis data, we also observe that there are a number of well-known cancer associated signaling pathways (mainly cancer), immune signaling pathway, critical metabolic associated pathways, cell cycle, ubiquitin-proteasomal signaling pathways, and p53 signaling. Network-level study of pathways and their components CD40LG as the potential gene where CD40LG is directly affecting 10 pathways and most of them are the parts of immune system and known to control a number of leading human diseases including cancers.

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Comparative Study of Gene Expression Profiling Unravels Functions Associated with Pathogenesis of Dengue Infection

Cited by 14 publications

References 0 publications

Gene Expression Profiling of Early Acute Febrile Stage of Dengue Infection and Its Comparative Analysis With Streptococcus pneumoniae Infection

Gene Expression Profiling of Early Acute Febrile Stage of Dengue Infection and Its Comparative Analysis With Streptococcus pneumoniae Infection

In-Silico Study of Immune System Associated Genes in Case of Type-2 Diabetes With Insulin Action and Resistance, and/or Obesity

Study of APOBEC3B focused breast cancer pathways and the clinical relevance

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