Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond.
Sign Up to like & getrecommendations! Published in 2017 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7027-8_7
Abstract: The analysis of gene sets (in a form of functionally related genes or pathways) has become the method of choice for extracting the strongest signals from omics data. The motivation behind using gene sets instead… read more here.
Keywords: signals omics; strongest signals; extracting strongest; gene ... See more keywords
Shifts in Ribosome Engagement Impact Key Gene Sets in Neurodevelopment and Ubiquitination in Rett Syndrome.
Sign Up to like & getrecommendations! Published in 2020 at "Cell reports"
DOI: 10.1016/j.celrep.2020.02.107
Abstract: Regulation of translation during human development is poorly understood, and its dysregulation is associated with Rett syndrome (RTT). To discover shifts in mRNA ribosomal engagement (RE) during human neurodevelopment, we use parallel translating ribosome affinity… read more here.
Keywords: gene sets; ubiquitination; key gene; rett syndrome ... See more keywords
SA19 GENE EXPRESSION SIGNATURES FROM PERIPHERAL BLOOD DISCRIMINATE THE MAJOR PSYCHOSES
Sign Up to like & getrecommendations! Published in 2019 at "European Neuropsychopharmacology"
DOI: 10.1016/j.euroneuro.2017.08.091
Abstract: Background Bipolar Disorder (BD) is a complex and highly heritable psychiatric disorder with a world-wide prevalence near 1%. There is converging evidence from genetic, molecular, and clinical studies of BD that implicate numerous neurotransmitter and… read more here.
Keywords: differential expression; peripheral blood; expression; gene ... See more keywords
Monoamine and neuroendocrine gene-sets associate with frustration-based aggression in a gender-specific manner
Sign Up to like & getrecommendations! Published in 2020 at "European Neuropsychopharmacology"
DOI: 10.1016/j.euroneuro.2017.11.016
Abstract: Investigating phenotypic heterogeneity in aggression and understanding the molecular biological basis of aggression subtypes may lead to new prevention and treatment options. In the current study, we evaluated the taxonomy of aggression and examined specific… read more here.
Keywords: frustration; aggression subtypes; factor; aggression ... See more keywords
Human placental gene sets improve analysis of placental pathologies and link trophoblast and cancer invasion genes.
Sign Up to like & getrecommendations! Published in 2021 at "Placenta"
DOI: 10.1016/j.placenta.2021.06.011
Abstract: INTRODUCTION Interpretation of gene expression uses set enrichment or overrepresentation methods that depend on sets of annotated genes, such as the popular Gene Ontology. The placenta is understudied relative to other major organs creating a… read more here.
Keywords: ontology; placental pathologies; human placental; placental gene ... See more keywords
Genetic predictors of gene expression associated with psychiatric comorbidity in patients with inflammatory bowel disease - A pilot study.
Sign Up to like & getrecommendations! Published in 2021 at "Genomics"
DOI: 10.1016/j.ygeno.2021.02.001
Abstract: BACKGROUND Inflammatory bowel disease (IBD) affects millions of people in North America, and patients with IBD have a high incidence of psychiatric comorbidities (PC). The genetic mechanisms underlying the link are, in general, poorly understood.… read more here.
Keywords: bowel disease; inflammatory bowel; study; gene ... See more keywords
Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia, and bipolar disorder
Sign Up to like & getrecommendations! Published in 2019 at "Translational Psychiatry"
DOI: 10.1038/s41398-019-0488-4
Abstract: Individuals affected with different neuropsychiatric disorders such as autism (AUT), schizophrenia (SCZ) and bipolar disorder (BPD), may share similar clinical manifestations, suggesting shared genetic influences and common biological mechanisms underlying these disorders. Using brain transcriptome… read more here.
Keywords: gene sets; expression; aut scz; gene ... See more keywords
DECO: a framework for jointly analyzing de novo and rare case/control variants, and biological pathways
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbab067
Abstract: MOTIVATION Rare variant-based analyses are beginning to identify risk genes for neuropsychiatric disorders and other diseases. However, the identified genes only account for a fraction of predicted causal genes. Recent studies have shown that rare… read more here.
Keywords: control variants; rare case; case control; gene ... 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
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes.
Sign Up to like & getrecommendations! Published in 2023 at "Nucleic acids research"
DOI: 10.1093/nar/gkad289
Abstract: Gene definitions and identifiers can be painful to manage-more so when trying to include gene function annotations as this can be highly context-dependent. Creating groups of genes or gene sets can help provide such context,… read more here.
Keywords: mygeneset info; info interactive; interactive programmatic; user created ... See more keywords
GLassonet: Identifying Discriminative Gene Sets among Molecular Subtypes of Breast Cancer.
Sign Up to like & getrecommendations! Published in 2022 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2022.3220623
Abstract: Breast cancer is a heterogeneous disease caused by various alterations in the genome or transcriptome. Molecular subtypes of breast cancer have been reported, but useful biomarkers remain to be identified to uncover underlying biological mechanisms… read more here.
Keywords: breast cancer; glassonet; cancer; gene sets ... See more keywords