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SpatialGE is a User-Friendly Web Application that Facilitates Spatial Transcriptomics Data Analysis

ABSTRACT: Spatial transcriptomics (ST) is a powerful tool for understanding tissue biology and disease mechanisms. However, the advanced data analysis and programming skills required can hinder researchers from realizing of the full potential of ST. To address this, we developed spatialGE, a web application that simplifies the analysis of ST data. The application spatialGE provided a user-friendly interface that guides users without programming expertise through various analysis pipelines, including quality control, normalization, domain detection, phenotyping, and multiple spatial analyses. It also enabled comparative analysis among samples and supported various ST technologies. The utility of spatialGE was demonstrated through its application in studying the tumor microenvironment of two data sets: 10X Visium samples from a cohort of melanoma metastasis and Nanostring CosMx fields of vision from a cohort of Merkel cell carcinoma samples. These results support the ability of spatialGE to identify spatial gene expression patterns that provide valuable insights into the tumor microenvironment and highlight its utility in democratizing ST data analysis for the wider scientific community.

ORGANISM(S): Homo sapiens

PROVIDER: GSE271422 | GEO | 2024/11/21

REPOSITORIES: GEO

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Project description:Background:Depression, as one of the most prevalent mental disorders, is expected to become a leading cause of disability. While evidence-based treatments are not always easily accessible, Internet-based information and self-help appears as a promising approach to improve the strained supply situation by avoiding barriers of traditional offline treatment. User experience in the domain of mental problems therefore emerges as an important research topic. The aim of our study is to investigate the impact of depressive symptoms on subjective and objective measures of web user experience. Method:In this two-part online study (Ntotal = 721) we investigate the relationship between depressive symptoms of web users and basic website characteristics (i.e., content, subjective and objective usability, aesthetics). Participants completed search and memory tasks on different fully-functional websites. In addition, they were asked to evaluate the given websites with standardized measures and were screened for symptoms of depression using the PHQ-9. We used structural equation modeling (SEM) to determine whether depression severity affects users' perception of and performance in using information websites. Results:We found significant associations between depressive symptoms and subjective user experience, specifically of website content, usability, and aesthetics, as well as an effect of content perception on the overall appraisal of a website in terms of the intention to visit it again. Small yet significant negative effects of depression severity on all named subjective website evaluations were revealed, leading to an indirect negative effect on the intention to revisit a website via impaired content perceptions. However, objective task performance was not influenced by depressiveness of users. Discussion:Depression emerges as capable of altering the subjective perception of a website to some extend with respect to the main features content, usability, and aesthetics. The user experience of a website is crucial, especially as it facilitates revisiting a website and thus might be relevant in avoiding drop-out in online interventions. Thus, the biased impression of persons affected by symptoms of depression and resulting needs of those users should be considered when designing and evaluating E-(Mental)-Health-platforms. The high prevalence of some mental disorders such as depression in the general population stresses the need for further investigations of the found effects.

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SpatialGE is a User-Friendly Web Application that Facilitates Spatial Transcriptomics Data Analysis

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