Protein Network Analysis of Whole Exome Sequencing of Severe Preeclampsia

Schuster, Jessica; Tollefson, George A.; Zarate, Valeria; Agudelo, Anthony; Stabila, Joan; Ragavendran, Ashok; Padbury, Jamés F.; Uzun, Alper

doi:10.3389/fgene.2021.765985

Cited by 4 publications

(3 citation statements)

References 69 publications

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“…Demonstrating VGC's capabilities, we present an example using whole exome sequencing data from preeclamptic patients and term mothers. The dataset includes 143 samples: 61 early onset severe preeclamptic cases and 82 term mother controls [16]. Through VGC, we offer a detailed analysis of this dataset, emphasizing major trends, statistical findings, and key outcomes aligned with our research goals.…”

Section: Resultsmentioning

confidence: 99%

Variant Graph Craft (VGC): A Comprehensive Tool for Analyzing Genetic Variation and Identifying Disease-Causing Variants

Li,

Yang,

Carneiro

et al. 2023

Preprint

Self Cite

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The Variant Call Format (VCF) file is providing a structured and comprehensive text file that contains essential information about variant positions in the genome, as well as other critical details, such as alleles, genotype calls, and quality scores. Due to its rich data and format, the VCF file has become an increasingly popular resource for researchers and clinicians alike, enabling them to interpret and understand genomic variation data. However, analyzing and visualizing these files poses significant challenges, demanding access to diverse resources and a robust set of features for in-depth exploration. We introduce Variant Graph Craft (VGC), a VCF file visualization and analysis tool offering a wide range of features for exploring genetic variations, including extraction of variant data, intuitive visualization of variants, and the provision of a graphical representation of samples, complete with genotype information. Furthermore, VGC seamlessly integrates with external resources to offer valuable insights into gene function and variant frequencies in sample data. VGC offers gene function and pathway information from Molecular Signatures Database (MSigDB) for GO terms, as well as KEGG, Biocarta, Pathway Interaction Database, and Reactome. Additionally, the tool also provides a dynamic link to gnomAD for variant information, and includes ClinVar data for pathogenic variant information. VGC operates locally, assuring users of data security and privacy by eliminating the need for cloud-based VCF uploads. It supports the Human Genome Assembly Hg37, ensuring compatibility with a wide range of data sets. With its versatility, VGC accommodates various approaches exploring genetic variation data, and can be tailored to the specific needs of the user by using optional phenotype input data. In conclusion, VGC is a useful resource for exploring genetic variation in a secure and user-friendly environment. With its user-tailored set of features, this tool enables researchers and clinicians to easily explore and understand genomic variation data in a comprehensive and accessible manner. From identifying specific genetic mutations to analyzing patterns of variation across the genome, the VCF file visualization and analysis tool is an essential tool for those working in the field of genomics. VGC is freely available athttps://sites.brown.edu/gmilab/variantgraphcraft/

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Section: Resultsmentioning

confidence: 99%

Variant Graph Craft (VGC): A Comprehensive Tool for Analyzing Genetic Variation and Identifying Disease-Causing Variants

Li,

Yang,

Carneiro

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

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“…Fibronectin 1 (FN1) is a glycoprotein that is involved in cell adhesion and cell spreading and is widely distributed in healthy membranes, vascular structures, and smooth muscle cell layers. [25][26][27] The plasma levels of FN1, which may be the best marker for vascular endothelial injury during PE, are increased in patients with PE. [28] Multiple studies have shown that FN1 is related to the pathogenesis of PE, and FN1 can be used as a potential marker in the diagnosis of PE.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics identification and validation of maternal blood biomarkers and immune cell infiltration in preeclampsia: An observational study

Wang,

Li,

Rong

et al. 2024

Medicine

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Preeclampsia (PE) is a pregnancy complication characterized by placental dysfunction. However, the relationship between maternal blood markers and PE is unclear. It is helpful to improve the diagnosis and treatment of PE using new biomarkers related to PE in the blood. Three PE-related microarray datasets were obtained from the Gene Expression Synthesis database. The limma software package was used to identify differentially expressed genes (DEGs) between PE and control groups. Least absolute shrinkage and selection operator regression, support vector machine, random forest, and multivariate logistic regression analyses were used to determine key diagnostic biomarkers, which were verified using clinical samples. Subsequently, functional enrichment analysis was performed. In addition, the datasets were combined for immune cell infiltration analysis and to determine their relationships with core diagnostic biomarkers. The diagnostic performance of key genes was evaluated using the receiver operating characteristic (ROC) curve, C-index, and GiViTi calibration band. Genes with potential clinical applications were evaluated using decision curve analysis (DCA). Seventeen DEGs were identified, and 6 key genes (FN1, MYADM, CA6, PADI4, SLC4A10, and PPP4R1L) were obtained using 3 types of machine learning methods and logistic regression. High diagnostic performance was found for PE through evaluation of the ROC, C-index, GiViti calibration band, and DCA. The 2 types of immune cells (M0 macrophages and activated mast cells) were significantly different between patients with PE and controls. All of these genes except SLC4A10 showed significant differences in expression levels between the 2 groups using quantitative reverse transcription-polymerase chain reaction. This model used 6 maternal blood markers to predict the occurrence of PE. The findings may stimulate ideas for the treatment and prevention of PE.

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“…These findings indicate that a multifaceted interplay of susceptibility factors is likely, potentially resulting in distinct patterns of preeclampsia. Supporting this concept, Schuster et al documented groups of patients exhibiting common gene and protein networks linked to severe preeclampsia ( 208 ).…”

Section: Endothelium In Pregnancymentioning

confidence: 99%

Pregnancy as a susceptible state for thrombotic microangiopathies

Frimat,

Gnemmi,

Stichelbout

et al. 2024

Front. Med.

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Pregnancy and the postpartum period represent phases of heightened vulnerability to thrombotic microangiopathies (TMAs), as evidenced by distinct patterns of pregnancy-specific TMAs (e.g., preeclampsia, HELLP syndrome), as well as a higher incidence of nonspecific TMAs, such as thrombotic thrombocytopenic purpura or hemolytic uremic syndrome, during pregnancy. Significant strides have been taken in understanding the underlying mechanisms of these disorders in the past 40 years. This progress has involved the identification of pivotal factors contributing to TMAs, such as the complement system, ADAMTS13, and the soluble VEGF receptor Flt1. Regardless of the specific causal factor (which is not generally unique in relation to the usual multifactorial origin of TMAs), the endothelial cell stands as a central player in the pathophysiology of TMAs. Pregnancy has a major impact on the physiology of the endothelium. Besides to the development of placenta and its vascular consequences, pregnancy modifies the characteristics of the women’s microvascular endothelium and tends to render it more prone to thrombosis. This review aims to delineate the distinct features of pregnancy-related TMAs and explore the contributing mechanisms that lead to this increased susceptibility, particularly influenced by the “gravid endothelium.” Furthermore, we will discuss the potential contribution of histopathological studies in facilitating the etiological diagnosis of pregnancy-related TMAs.

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Protein Network Analysis of Whole Exome Sequencing of Severe Preeclampsia

Cited by 4 publications

References 69 publications

Variant Graph Craft (VGC): A Comprehensive Tool for Analyzing Genetic Variation and Identifying Disease-Causing Variants

Variant Graph Craft (VGC): A Comprehensive Tool for Analyzing Genetic Variation and Identifying Disease-Causing Variants

Bioinformatics identification and validation of maternal blood biomarkers and immune cell infiltration in preeclampsia: An observational study

Pregnancy as a susceptible state for thrombotic microangiopathies

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