Summarizing RNA-Seq Data or Differentially Expressed Genes Using Gene Set, Network, or Pathway Analysis.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1307-8_9
Abstract: The main purpose of pathway or gene set analysis methods is to provide mechanistic insight into the large amount of data produced in high-throughput studies. These tools were developed for gene expression analyses, but they… read more here.
Keywords: gene set; summarizing rna; pathway; pathway analysis ... See more keywords
A 20-Gene Set Predictive of Progression to Severe Dengue
Sign Up to like & getrecommendations! Published in 2019 at "Cell Reports"
DOI: 10.1016/j.celrep.2019.01.033
Abstract: Summary There is a need to identify biomarkers predictive of severe dengue. Single-cohort transcriptomics has not yielded generalizable results or parsimonious, predictive gene sets. We analyzed blood samples of dengue patients from seven gene expression… read more here.
Keywords: gene set; progression severe; dengue; gene ... See more keywords
Gene set analysis and reduction for a continuous phenotype: Identifying markers of birth weight variation based on embryonic stem cells and immunologic signatures
Sign Up to like & getrecommendations! Published in 2019 at "Computers in biology and medicine"
DOI: 10.1016/j.compbiomed.2019.103389
Abstract: BACKGROUND Gene set analysis is a popular approach to examine the association between a predefined gene set and a phenotype. Few methods have been developed for a continuous phenotype. However, often not all the genes… read more here.
Keywords: gene set; reduction; gene; continuous phenotype ... See more keywords
SU3 THE ROLE OF A NEURONAL DIFFERENTIATION GENE-SET IN ADHD SUSCEPTIBILITY
Sign Up to like & getrecommendations! Published in 2019 at "European Neuropsychopharmacology"
DOI: 10.1016/j.euroneuro.2017.08.192
Abstract: Background ADHD is a common neuropsychiatric disorder, it is highly heritable and polygenic, with a great number of combinations of variants, each with small effects, involved in its underlying molecular processes. However, the identification of… read more here.
Keywords: gene set; gene; adhd susceptibility; neuronal differentiation ... See more keywords
Gene set enrichment analysis and expression pattern exploration implicate an involvement of neurodevelopmental processes in bipolar disorder.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of affective disorders"
DOI: 10.1016/j.jad.2017.11.068
Abstract: BACKGROUND Bipolar disorder (BD) is a common and highly heritable disorder of mood. Genome-wide association studies (GWAS) have identified several independent susceptibility loci. In order to extract more biological information from GWAS data, multi-locus approaches… read more here.
Keywords: gene set; set enrichment; expression; bipolar disorder ... See more keywords
Gene-set analysis shows association between FMRP targets and autism spectrum disorder
Sign Up to like & getrecommendations! Published in 2017 at "European Journal of Human Genetics"
DOI: 10.1038/ejhg.2017.55
Abstract: Autism spectrum disorder (ASD) is a heterogeneous group of disorders characterized by problems with social interaction, communication, and repetitive and restricted behavior. Despite its high heritability and the substantial progress made in elucidating genetic associations,… read more here.
Keywords: gene set; fmrp targets; spectrum disorder; gene ... See more keywords
Pairwise common variant meta-analyses of schizophrenia with other psychiatric disorders reveals shared and distinct gene and gene-set associations
Sign Up to like & getrecommendations! Published in 2020 at "Translational Psychiatry"
DOI: 10.1038/s41398-020-0817-7
Abstract: The complex aetiology of schizophrenia is postulated to share components with other psychiatric disorders. We investigated pleiotropy amongst the common variant genomics of schizophrenia and seven other psychiatric disorders using a multimarker association test. Transcriptomic… read more here.
Keywords: schizophrenia psychiatric; gene set; common variant; psychiatric disorders ... See more keywords
Conditional and interaction gene-set analysis reveals novel functional pathways for blood pressure
Sign Up to like & getrecommendations! Published in 2018 at "Nature Communications"
DOI: 10.1038/s41467-018-06022-6
Abstract: Gene-set analysis provides insight into which functional and biological properties of genes are aetiologically relevant for a particular phenotype. But genes have multiple properties, and these properties are often correlated across genes. This can cause… read more here.
Keywords: gene set; blood; gene; conditional interaction ... See more keywords
GSCA: an integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac558
Abstract: Cancer initiation and progression are likely caused by the dysregulation of biological pathways. Gene set analysis (GSA) could improve the signal-to-noise ratio and identify potential biological insights on the gene set level. However, platforms exploring… read more here.
Keywords: pharmacogenomic immunogenomic; analysis; gene set; genomic pharmacogenomic ... See more keywords
GSOAP: a tool for visualization of gene set over-representation analysis
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa001
Abstract: Abstract Motivation Gene sets over-representation analysis (GSOA) is a common technique of enrichment analysis that measures the overlap between a gene set and selected instances (e.g. pathways). Despite its popularity, there is currently no established… read more here.
Keywords: gene set; analysis; visualization; gsoap ... See more keywords
Differential Gene Set Enrichment Analysis: A statistical approach to quantify the relative enrichment of two gene sets.
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa658
Abstract: MOTIVATION Gene Set Enrichment Analysis (GSEA) is an algorithm widely used to identify statistically enriched gene sets in transcriptomic data. However, GSEA cannot examine the enrichment of two gene sets or pathways relative to one… read more here.
Keywords: gene set; enrichment analysis; dgsea; set enrichment ... See more keywords