Identifying Significantly Impacted Pathways and Putative Mechanisms with iPathwayGuide

Ahsan, Syed F.; Drăghici, Sorin

doi:10.1002/cpbi.24

Cited by 85 publications

(77 citation statements)

References 26 publications

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“…We used iPathway Guide software [38][39][40][41] to identify significantly and differentiallyexpressed genes between groups in our cohort. Genes were considered to be significant if the | logFC| > 0.60 and they had an adjusted false discovery rate (FDR) <0.30.…”

Section: Analysis Of Gene Expression In Individuals Living In Povertymentioning

confidence: 99%

The association between poverty and gene expression within peripheral blood mononuclear cells in a diverse Baltimore City cohort

et al. 2020

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Socioeconomic status (SES), living in poverty, and other social determinants of health contribute to health disparities in the United States. African American (AA) men living below poverty in Baltimore City have a higher incidence of mortality when compared to either white males or AA females living below poverty. Previous studies in our laboratory and elsewhere suggest that environmental conditions are associated with differential gene expression (DGE) patterns in peripheral blood mononuclear cells (PBMCs). DGE have also been associated with hypertension and cardiovascular disease (CVD) and correlate with race and sex. However, no studies have investigated how poverty status associates with DGE between male and female AAs and whites living in Baltimore City. We examined DGE in 52 AA and white participants of the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) cohort, who were living above or below 125% of the 2004 federal poverty line at time of sample collection. We performed a microarray to assess DGE patterns in PBMCs from these participants. AA males and females living in poverty had the most genes differentially-expressed compared with above poverty controls. Gene ontology (GO) analysis identified unique and overlapping pathways related to the endosome, single-stranded RNA binding, long-chain fatty-acyl-CoA biosynthesis, toll-like receptor signaling, and others within AA males and females living in poverty and compared with their above poverty controls. We performed RT-qPCR to validate top differentially-expressed genes in AA males. We found that KLF6, DUSP2, RBM34, and CD19 are expressed at significantly lower levels in AA males in poverty and KCTD12 is higher compared to above poverty controls. This study serves as an additional link to better understand the gene expression response in peripheral blood mononuclear cells in those living in poverty.

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Section: Analysis Of Gene Expression In Individuals Living In Povertymentioning

confidence: 99%

The association between poverty and gene expression within peripheral blood mononuclear cells in a diverse Baltimore City cohort

et al. 2020

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“…The network of biological processes among the differentially expressed genes and villous trophoblast differentiation pathways was determined by BiNGO [98]. Pathway Studio 9.0 and iPathwayGuide [123][124][125] were used for pathway analysis. iPathwayGuide scores the pathways by means of the Impact Analysis method [124,126,127].…”

Section: Functional Annotation and Pathway Analysismentioning

confidence: 99%

Placenta-Specific Genes, Their Regulation During Villous Trophoblast Differentiation and Dysregulation in Preterm Preeclampsia

Szilágyi

Gelencser

Romero

et al. 2020

IJMS

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The human placenta maintains pregnancy and supports the developing fetus by providing nutrition, gas-waste exchange, hormonal regulation, and an immunological barrier from the maternal immune system. The villous syncytiotrophoblast carries most of these functions and provides the interface between the maternal and fetal circulatory systems. The syncytiotrophoblast is generated by the biochemical and morphological differentiation of underlying cytotrophoblast progenitor cells. The dysfunction of the villous trophoblast development is implicated in placenta-mediated pregnancy complications. Herein, we describe gene modules and clusters involved in the dynamic differentiation Int.Int. J. Mol. Sci. 2020, 21, 628 2 of 27 of villous cytotrophoblasts into the syncytiotrophoblast. During this process, the immune defense functions are first established, followed by structural and metabolic changes, and then by peptide hormone synthesis. We describe key transcription regulatory molecules that regulate gene modules involved in placental functions. Based on transcriptomic evidence, we infer how villous trophoblast differentiation and functions are dysregulated in preterm preeclampsia, a life-threatening placenta-mediated obstetrical syndrome for the mother and fetus. In the conclusion, we uncover the blueprint for villous trophoblast development and its impairment in preterm preeclampsia, which may aid in the future development of non-invasive biomarkers for placental functions and early identification of women at risk for preterm preeclampsia as well as other placenta-mediated pregnancy complications.

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“…The dynamic interface in the application allows users to fine tune filters without having to worry about copious amounts of lag time. One of the more compelling features of the application is assessing samples using GO Term and Pathway Impact Analysis (Ahsan & Drăghici, ).…”

Section: Commentarymentioning

confidence: 99%

“…These concerns can be addressed by utilizing the variant assessment application iVariantGuide by Advaita Bioinformatics. This Web‐based tool uniquely provides dynamic and interactive capabilities with little lag time, along with unique Pathway Ω impact (Ahsan & Drăghici, ) and Gene Ontology (GO) analyses based on the mutations present in the patient's DNA.…”

Section: Introductionmentioning

confidence: 99%

Utilizing iVariantGuide for Variant Assessment of Next‐Generation Sequencing

Chaudhry

Tainsky

2019

CP in Bioinformatics

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Molecular genetic testing provides the capability for personalized prediction, diagnosis, and pharmacological treatments of disease and disorders. Variant assessment of next‐generation sequencing (NGS) is a crucial component of genetic testing for clinicians to counsel patients on risk and management. The iVariantGuide application is a dynamic Web‐based application made for the tertiary analysis of NGS. Along with variant assessment, iVariantGuide provides a unique interactive pathway impact analysis of genetic variants, as well as a unique Gene Ontology (GO) analysis. Here we provide a step‐by‐step guide on how to utilize iVariantGuide, employing a publicly available NGS dataset consisting of a cohort of germline DNAs from high‐risk serous ovarian cancer (OVCA) patients. The application will be used to exhibit the ease in filtering down to a set of compelling novel variants and their impact on biological pathways and GO terms. © 2019 by John Wiley & Sons, Inc.

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Identifying Significantly Impacted Pathways and Putative Mechanisms with iPathwayGuide

Cited by 85 publications

References 26 publications

The association between poverty and gene expression within peripheral blood mononuclear cells in a diverse Baltimore City cohort

The association between poverty and gene expression within peripheral blood mononuclear cells in a diverse Baltimore City cohort

Placenta-Specific Genes, Their Regulation During Villous Trophoblast Differentiation and Dysregulation in Preterm Preeclampsia

Utilizing iVariantGuide for Variant Assessment of Next‐Generation Sequencing

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