Identification of differentially expressed genes and their major pathways among the patient with COVID-19, cystic fibrosis, and chronic kidney disease

Babu, Golap; Nobel, Fahim Alam

doi:10.1016/j.imu.2022.101038

Cited by 7 publications

(4 citation statements)

References 85 publications

(83 reference statements)

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“…On the other hand, miRNA was only associated with MTX1 genes (Figure 10 ). This type of network has a potential implication in many research projects concerning the prediction of disease genes, taking into account factors such as disease loci, gene-disease phenotypic relationships, and disease-specific changes in gene expression [ 29 ]. Using DSigDB, the top 10 therapeutic interventions targeting the DEG were identified (Table 4 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of Differentially Expressed Genes and Protein-Protein Interaction in Patients With COVID-19 and Diabetes Peripheral Neuropathy: A Bioinformatics and System Biology Approach

Nobel,

Kamruzzaman,

Asaduzzaman

et al. 2024

Cureus

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The coronavirus disease 2019 (COVID-19) pandemic has had a significant impact globally, resulting in a higher death toll and persistent health issues for survivors, particularly those with pre-existing medical conditions. Numerous studies have demonstrated a strong correlation between catastrophic COVID-19 results and diabetes. To gain deeper insights, we analysed the transcriptome dataset from COVID-19 and diabetic peripheral neuropathic patients. Using the R programming language, differentially expressed genes (DEGs) were identified and classified based on up and down regulations. The overlaps of DEGs were then explored between these groups. Functional annotation of those common DEGs was performed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Bio-Planet, Reactome, and Wiki pathways. A protein-protein interaction (PPI) network was created with bioinformatics tools to understand molecular interactions. Through topological analysis of the PPI network, we determined hub gene modules and explored gene regulatory networks (GRN). Furthermore, the study extended to suggesting potential drug molecules for the identified mutual DEG based on the comprehensive analysis. These approaches may contribute to understanding the molecular intricacies of COVID-19 in diabetic peripheral neuropathy patients through insights into potential therapeutic interventions.

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Section: Discussionmentioning

confidence: 99%

Identification of Differentially Expressed Genes and Protein-Protein Interaction in Patients With COVID-19 and Diabetes Peripheral Neuropathy: A Bioinformatics and System Biology Approach

Nobel,

Kamruzzaman,

Asaduzzaman

et al. 2024

Cureus

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“…The interactive online tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) was used to identify DEGs. This package compares infected SCA patients with healthy controls to detect DEGs using the GEO query and limma R tools from the Bioconductor, an open-source software project based on the R program (Babu and Nobel 2022). The signi cant genes' up-regulated and down-regulated were categorized based on Log2 (fold change) values, > 1.5 and < − 1.5, respectively.…”

Section: Identi Cation Of Differentially Expressed Genes (Degs)mentioning

confidence: 99%

Identification of proinflammatory pathways and promising bioactive polyphenols for the treatment of sickle cell anemia by in silico study and network pharmacology

Pérez,

Lázaro,

Puentes

et al. 2024

Preprint

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Sickle cell anemia (SCA) is an autosomal recessive Mendelian trait characterized by symptoms that include acute and chronic pain, chest syndrome, pulmonary hypertension, stroke, kidney disease, and vaso-occlusive crises (VOCs), all of which worsen with age; VOCs are the leading cause of hospitalization and premature death in SCA patients. Currently, despite the existence of treatments for SCA, the negative consequences of VOCs’ chronic inflammatory state demand the exploration of alternative methods of control. For this reason, the goal of this research was to find novel pathways and promising bioactive polyphenols for the treatment of SCA using a combination of network pharmacology and in silico approaches; due to polyphenols, they have shown widely reported anti-inflammatory properties. Initially, hub genes associated with inflammatory processes in SCA were identified by extracting differentially expressed genes (DEGs) from a publicly available GEO dataset (GSE53441), followed by their validation through system biology analysis, Polyphenols with anti-inflammatory activity were selected from natural product databases; finally, molecular docking and dynamics were performed with the polyphenols and the key protein derived from the selected hub genes. As a result, 10 genes associated with the Type I interferon (IFN-I) pathway in SCA were identified (MX1, FIT1, IFIT3, STAT1, ISG15, GBP1, OAS1, OAS2, OAS3, and RSAD); among them, STAT1 was selected as a central hub gene by regulating the expression of the rest. Docking and dynamics studies showed good binding energies among STAT1 and the fifteen polyphenolic extracted compounds, with quercetin, diosmetin, and fisetin showing the lowest binding energies. Identified flavonoids have been described in the past as compounds having anti-inflammatory and antioxidant features, as well as possible alternatives for SCA treatment.

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“…The interactive online tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) was used to identify DEGs. This package compares infected SCA patients with healthy controls to detect DEGs using the GEO query and limma R tools from the Bioconductor, an open-source software project based on the R program [31]. The signi cant genes' up-regulated and down-regulated were categorized based on Log2 (fold change) values, > 1.5 and < − 1.5, respectively.…”

Section: Identi Cation Of Differentially Expressed Genes (Degs)mentioning

confidence: 99%

Network pharmacology and an in silico-based study to identify proinflammatory pathways and promising bioactive polyphenols for the treatment of sickle cell anemia

Pérez,

Lázaro,

Puentes

et al. 2024

Preprint

View full text Add to dashboard Cite

Sickle cell anemia (SCA) is a disease transmitted as an autosomal recessive Mendelian trait. It causes symptoms that worsen with age, such as acute and chronic pain, chest syndrome, pulmonary hypertension, stroke, kidney disease, and vaso-occlusive crises (VOCs), which are the leading cause of hospitalization and premature death. Although there are existing treatments to manage it, side effects related to VOCs such as patients’ inflammatory state requires the review of options for its control. In this sense, the study of polyphenols represents a potential alternative for the treatment of ACS due to their widely reported anti-inflammatory capacities. This research identified hub genes associated with inflammatory processes in SCA by extracting differentially expressed genes (DEGs) in a GEO dataset collection. Then, polyphenols with anti-inflammatory activity were selected from natural product databases, subsequently, molecular docking was performed with the polyphenols and the key protein derived from the selected hub genes. Finally, molecular dynamics were performed on the promising complexes. The comparative analysis allowed us to find 10 genes associated with proinflammatory pathways in SCA (MX1, FIT1, IFIT3, STAT1, ISG15, GBP1, OAS1, OAS2, OAS3, and RSAD); among them, STAT1 was selected as a central gene by regulating the expression of the rest. Docking and dynamics studies showed good binding energies among STAT1 and the fifteen polyphenolic extracted compounds, with quercetin, diosmetin, and fisetin showing the lowest binding energies. These flavonoids have been described in the past as compounds having anti-inflammatory and antioxidant features, as well as possible alternatives for SCA treatment.

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Identification of differentially expressed genes and their major pathways among the patient with COVID-19, cystic fibrosis, and chronic kidney disease

Cited by 7 publications

References 85 publications

Identification of Differentially Expressed Genes and Protein-Protein Interaction in Patients With COVID-19 and Diabetes Peripheral Neuropathy: A Bioinformatics and System Biology Approach

Identification of Differentially Expressed Genes and Protein-Protein Interaction in Patients With COVID-19 and Diabetes Peripheral Neuropathy: A Bioinformatics and System Biology Approach

Identification of proinflammatory pathways and promising bioactive polyphenols for the treatment of sickle cell anemia by in silico study and network pharmacology

Network pharmacology and an in silico-based study to identify proinflammatory pathways and promising bioactive polyphenols for the treatment of sickle cell anemia

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