Unlabelled: The KGraph is a data visualization system that has been developed to display the complex relationships between the univariate and bivariate associations among an outcome of interest, a set of covariates, and a set of genetic factors, such as single nucleotide polymorphisms (SNPs). It allows for easy viewing and interpretation of genetic associations, correlations among covariates and SNPs, and information about the replication and cross-validation of the associations. The KGraph allows the user to more easily investigate multicollinearity and confounding through visualization of the multidimensional correlation structure underlying genetic associations. It emphasizes gene-environment and gene-gene interaction, both important components of any genetic system that are often overlooked in association frameworks.
Availability: http://www.epidkardia.sph.umich.edu/software/kgrapher
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1093/bioinformatics/btl510 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Highly multiplexed imaging reveals prognostic immune and stromal spatial biomarkers in breast cancer.
JCI Insight
January 2025
Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States of America.
Spatial profiling of tissues promises to elucidate tumor-microenvironment interactions and generate prognostic and predictive biomarkers. We analyzed single-cell, spatial data from three multiplex imaging technologies: cyclic immunofluorescence (CycIF) data we generated from 102 breast cancer patients with clinical follow-up, and publicly available imaging mass cytometry and multiplex ion-beam imaging datasets. Similar single-cell phenotyping results across imaging platforms enabled combined analysis of epithelial phenotypes to delineate prognostic subtypes among estrogen-receptor positive (ER+) patients.
View Article and Find Full Text PDFCorrelates of Impaired Timing Abilities in Schizophrenia: A Systematic Review.
J Nerv Ment Dis
December 2024
Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Section of Psychiatry, University of Genoa, Genoa, Italy.
This review aimed at summarizing the literature evidence on clinical, cognitive, and neurobiological correlates of impaired timing abilities in schizophrenia (SCZ). Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a systematic literature search was conducted in PubMed, EMBASE, and PsycInfo by looking at correlates between timing abilities and either symptom severity, cognition, and neurobiological data (imaging and electroencephalography) in individuals with SCZ, without restrictions on study design. A total of 45 articles were selected: associations were identified between impaired timing performance and positive, negative, and disorganization symptoms, as well as with executive functioning, working memory, and attention.
View Article and Find Full Text PDFPKCδ germline variants and genetic deletion in mice augment antitumor immunity through regulation of myeloid cells.
Cancer Immunol Res
January 2025
University of Chicago, Chicago, IL, United States.
Based on the notion that hypomorphic germline genetic variants are linked to autoimmune diseases, we reasoned that novel targets for cancer immunotherapy might be identified through germline variants associated with greater T-cell infiltration into tumors. Here, we report that while investigating germline polymorphisms associated with a tumor immune gene signature, we identified PKCδ as a candidate. Genetic deletion of PKCδ in mice resulted in improved endogenous antitumor immunity and increased efficacy of anti-PD-L1.
View Article and Find Full Text PDFNarciclasine attenuates sepsis-associated acute kidney injury through the ESR1/S100A11 axis.
Funct Integr Genomics
January 2025
Department of Emergency and Critical Care Medicine, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210028, People's Republic of China.
Narciclasine (Ncs) was effective in sepsis management due to its antioxidant properties. The present study dissected the protective effects of Ncs against sepsis-associated acute kidney injury (SA-AKI) and the molecular mechanisms. The SA-AKI mice were developed using cecum ligation and puncture and pretreated with Ncs and adenoviruses.
View Article and Find Full Text PDFGenome-wide association mapping for stay-green and stem reserve mobilization traits in wheat (Triticum aestivum L.) under combined heat and drought stress.
Protoplasma
January 2025
Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.
Stay-green (SG) and stem reserve mobilization (SRM) are two significant mutually exclusive traits, which contributes to grain-filling during drought and heat stress in wheat. The current research was conducted in a genome-wide association study (GWAS) panel consisting of 278 wheat genotypes of advanced breeding lines to find the markers linked with SG and SRM traits and also to screen the superior genotypes. SG and SRM traits, viz.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!