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Computational workflow for functional characterization of COVID-19 through secondary data analysis

ABSTRACT: Summary Standard transcriptomic analyses cannot fully capture the molecular mechanisms underlying disease pathophysiology and outcomes. We present a computational heterogeneous data integration and mining protocol that combines transcriptional signatures from multiple model systems, protein-protein interactions, single-cell RNA-seq markers, and phenotype-genotype associations to identify functional feature complexes. These feature modules represent a higher order multifeatured machines collectively working toward common pathophysiological goals. We apply this protocol for functional characterization of COVID-19, but it could be applied to many other diseases. For complete details on the use and execution of this protocol, please refer to Ghandikota et al. (2021). Graphical abstract Highlights • Steps for meta-analysis of multiple transcriptomic studies and protein interactions• Network analysis-based workflow to identify gene and functional modules• Data-driven higher-order functional features provide a basis for characterizing disease Standard transcriptomic analyses cannot fully capture the molecular mechanisms underlying disease pathophysiology and outcomes. We present a computational heterogeneous data integration and mining protocol that combines transcriptional signatures from multiple model systems, protein-protein interactions, single-cell RNA-seq markers, and phenotype-genotype associations to identify functional feature complexes. These feature modules represent a higher order multifeatured machines collectively working toward common pathophysiological goals. We apply this protocol for functional characterization of COVID-19, but it could be applied to many other diseases.

SUBMITTER: Ghandikota S

PROVIDER: S-EPMC8551262 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundAdults with chronic conditions are disproportionately burdened by COVID-19 morbidity and mortality. Although COVID-19 mobile health (mHealth) apps have emerged, research on attitudes toward using COVID-19 mHealth tools among those with chronic conditions is scarce.ObjectiveThis study aimed to examine attitudes toward COVID-19, identify determinants of COVID-19 mHealth tool use across demographic and health-related characteristics, and evaluate associations between chronic health conditions and attitudes toward using COVID-19 mHealth tools (eg, mHealth or web-based methods for tracking COVID-19 exposures, symptoms, and recommendations).MethodsWe used nationally representative data from the COVID-19 Impact Survey collected from April to June 2020 (n=10,760). Primary exposure was a history of chronic conditions, which were defined as self-reported diagnoses of cardiometabolic, respiratory, immune-related, and mental health conditions and overweight/obesity. Primary outcomes were attitudes toward COVID-19 mHealth tools, including the likelihood of using (1) a mobile phone app to track COVID-19 symptoms and receive recommendations; (2) a website to track COVID-19 symptoms, track location, and receive recommendations; and (3) an app using location data to track potential COVID-19 exposure. Outcome response options for COVID-19 mHealth tool use were extremely/very likely, moderately likely, or not too likely/not likely at all. Multinomial logistic regression was used to compare the likelihood of COVID-19 mHealth tool use between people with different chronic health conditions, with not too likely/not likely at all responses used as the reference category for each outcome. We evaluated the determinants of each COVID-19 mHealth intervention using Poisson regression.ResultsOf the 10,760 respondents, 21.8% of respondents were extremely/very likely to use a mobile phone app or a website to track their COVID-19 symptoms and receive recommendations. Additionally, 24.1% of respondents were extremely/very likely to use a mobile phone app to track their location and receive push notifications about whether they have been exposed to COVID-19. After adjusting for age, race/ethnicity, sex, socioeconomic status, and residence, adults with mental health conditions were the most likely to report being extremely/very or moderately likely to use each mHealth intervention compared to those without such conditions. Adults with respiratory-related chronic diseases were extremely/very (conditional odds ratio 1.16, 95% CI 1.00-1.35) and moderately likely (conditional odds ratio 1.23, 95% CI 1.04-1.45) to use a mobile phone app to track their location and receive push notifications about whether they have been exposed to COVID-19.ConclusionsOur study demonstrates that attitudes toward using COVID-19 mHealth tools vary widely across modalities (eg, web-based method vs app) and chronic health conditions. These findings may inform the adoption of long-term engagement with COVID-19 apps, which is crucial for determining their potential in reducing disparities in COVID-19 morbidity and mortality among individuals with chronic health conditions.

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Computational workflow for functional characterization of COVID-19 through secondary data analysis

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