Gene-set enrichment analysis is the key methodology for obtaining biological information from transcriptomic space’s statistical result. Since its introduction, Gene-set Enrichment analysis methods have obtained more reliable results and a wide...
Functional enrichment is a widely used method for interpreting experimental results by identifying classes of proteins/genes associated with certain biological functions, pathways, diseases, or phenotypes. Despite the variety of existing tools, most...
Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-Change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes f...
Fucoidan, a sulfated polysaccharide extracted from brown seaweed, has been proposed to effectively treat and prevent various viral infections. However, the mechanisms behind its antiviral activity are not completely understood. We investigate here th...
The increasing number of OMICs studies demands bioinformatic tools that aid in the analysis of large sets of genes or proteins to understand their roles in the cell and establish functional networks and pathways. In the last decade, over-representati...
Genome-wide association studies (GWAS) identified many association signals for metabolic syndrome (MetS). However, the understanding of its pathophysiology may be limited because of the complexity of the intertwined genetic factors that underlie diag...
The present study aimed to identify causative loci and genes enriched in pathways associated with canine obesity using a genome-wide association study (GWAS). The GWAS was first performed to identify candidate single-nucleotide polymorphisms (SNPs) a...
Characterising genomic variants is paramount in understanding the pathogenesis and heterogeneity of normal-karyotype acute myeloid leukaemia (AML-NK). In this study, clinically significant genomic biomarkers were ascertained using targeted DNA sequen...
Corynebacterium glutamicum is widely used for amino acid production. In the present study, 543 genes showed a significant change in their mRNA expression levels in l-lysine-producing C. glutamicum ATCC21300 than that in the wild-type C. glutamicum AT...
Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory...
As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Human selection and targeted breeding have produced an extraordinary diversity in these traits. Therefore, the i...
Abnormal accumulation of alpha synuclein (α-Syn) in sporadic and familial Parkinson’s disease (PD) may be a key step in its pathogenesis. In this study, the expression matrix of the GSE95427 dataset after α-Syn overexpression in hum...
Genome-wide association studies (GWAS) have identified genetic markers associated with type 2 diabetes mellitus (T2DM). Additionally, tissue-specific expression quantitative trait loci (eQTL) studies have revealed regulatory elements influencing gene...
A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea,...
Background: Involvement of the subventricular zone (SVZ) in glioblastoma is associated with poor prognosis and is associated with specific tumor-biological characteristics. The SVZ microenvironment can influence gene expression in glioblastoma cells...
Astrocytes have many important functions in the brain, but their roles in psychiatric disorders and their responses to psychotropic medications are still being elucidated. Here, we used gene enrichment analysis to assess the relationships between dif...
Acute lung injury occurs in 20–25% of cases following traumatic brain injury (TBI). We investigated changes in lung transcriptome expression post-TBI using animal models and bioinformatics. Employing unilateral controlled cortical impact for TB...
The reduced expression of the HCN1 ion channel in the somatosensory cortex (SSC) and mesolimbic dopamine deficiency are thought to be associated with the genesis of spike-wave discharges (SWDs) and comorbid depression in the WAG/Rij rat model of abse...
Drought stress is a significant abiotic factor influencing maize growth and development. Understanding the molecular mechanism of drought tolerance is critical to develop the drought tolerant genotype. The identification of the stress responsive gene...
SARS-CoV-2 uses ACE2 and TMPRSS2 to gain entry into the cell. However, recent studies have shown that SARS-CoV-2 may use additional host factors that are required for the viral lifecycle. Here we used publicly available datasets, CoV-associated genes...
Background: Carotenoids play essential nutritional and physiological roles in aquatic animals. Since aquatic species cannot synthesize carotenoids de novo, they must obtain these compounds from their diet to meet the physiological and adaptive requir...
Osteosarcoma is the most common subtype of primary bone cancer, affecting mostly adolescents. In recent years, several studies have focused on elucidating the molecular mechanisms of this sarcoma; however, its molecular etiology has still not been de...
Background: Severe burns activate systemic inflammation and lead to an increase in cytokine levels. Epigenetic elements are key regulators of inflammation; however, their involvement in severe burns has not been studied. In this work, we aimed to unv...
To study the evolution of gene function and a species, it is essential to characterize the tandem repetitive sequences distributed across the genome. Cas9-based enrichment combined with nanopore sequencing is an important technique for targeting repe...
The COVID-19 pandemic stemmed a parallel upsurge in the scientific literature about SARS-CoV-2 infection and its health burden. The Rat Genome Database (RGD) created a COVID-19 Disease Portal to leverage information from the scientific literature. In...
Background/Objectives: PRKACA alterations have clear diagnostic and biological roles in the fibrolamellar variant of hepatocellular carcinoma and a potential predictive role in that cancer type. However, the roles of PRKACA have not been comprehensiv...
Coronary artery disease (CAD) is a major cause of end-stage cardiac disease. Although profound efforts have been made to illuminate the pathogenesis, the molecular mechanisms of CAD remain to be analyzed. To identify the candidate genes in the advanc...
Selenium (Se) is an essential trace element for human health, and dietary Se intake is an effective supplement. Rich in nutrients and functional components with potential for Se enrichment, Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) is a Se...
MAGE (Meta-Analysis of Gene Expression) is a Python open-source software package designed to perform meta-analysis and functional enrichment analysis of gene expression data. We incorporate standard methods for the meta-analysis of gene expression st...
Glioblastomas are the most frequent primary brain tumors in adults. They show highly malignant behavior and devastating outcomes. Since there are still no targeted therapies available, median survival remains in the range of 12 to 15 months for gliob...
In recent years, perinatal stem cells, such as human amniotic epithelial cells (hAECs), have attracted increasing interest as a novel tool of stem cell-based high-throughput drug screening. In the present study, we investigated the bioactivities of s...
(1) Background: Information regarding gene expression profiles and the prognosis of community-acquired pneumonia (CAP) is scarce. We aimed to examine the differences in the gene expression profiles in peripheral blood at hospital admission between pa...
Gene expression differences can assist in characterizing important underlying genetic mechanisms between different phenotypic traits. However, when population-dense tissues are studied, the signals from scarce populations are diluted. Therefore, appr...
The human microbiome is a vast collection of microbial species that exist throughout the human body and regulate various bodily functions and phenomena. Of the microbial species that exist in the human microbiome, those within the archaea domain have...
Background: Adenomyosis is a gynaecological condition with limited evidence of negative impact to endometrial receptivity. It is commonly associated with endometriosis, which has been shown to alter endometrial expression patterns. Therefore, the can...
Background/Objectives: Bovine respiratory disease (BRD) is a common disease impacting cattle throughout the US. BRD is a multifactorial disease as disease risk varies with the genetic profile of the host, environmental conditions, and pathogen exposu...
Hepatocellular carcinoma (HCC) is associated with high mortality due to its inherent heterogeneity, aggressiveness, and limited therapeutic regimes. Herein, we analyzed 21 human HCC cell lines (HCC lines) to explore intertumor molecular diversity and...
The RNA-Seq and gene expression data of mature leaves under high temperature stress of Paeonia suffruticosa ‘Hu Hong’ were used to explore the key genes of heat tolerance of peony. The weighted gene co-expression network analysis (WGCNA)...
In recent decades, many efforts have been made to elucidate the genetic causes of non-syndromic cleft palate (nsCPO), a complex congenital disease caused by the interaction of several genetic and environmental factors. Since genome-wide association s...
Traditional gene set enrichment analysis falters when applied to large genomic domains, where neighboring genes often share functions. This spatial dependency creates misleading enrichments, mistaking mere physical proximity for genuine biological co...
Vestibular schwannoma (VS) is an intracranial tumor that commonly presents with tinnitus and hearing loss. To uncover the molecular mechanisms underlying VS-associated tinnitus, we applied next-generation sequencing (Illumina HiSeq) to formalin-fixed...
Changes in the atmospheric CO2 concentration influence plant growth and development by affecting the morphological structure and photosynthetic performance. Despite evidence for the macro-effects of elevated CO2 concentrations on plant morphology and...
Dpep is a cell-penetrating peptide targeting transcription factors ATF5, CEBPB, and CEBPD, and that selectively promotes the apoptotic death of multiple tumor cell types in vitro and in vivo. As such, it is a potential therapeutic. To better understa...
To understand complex diseases, high-throughput data are generated at large and multiple levels. However, extracting meaningful information from large datasets for comprehensive understanding of cell phenotypes and disease pathophysiology remains a m...
Alkali stress, a type of abiotic stress, severely inhibits plant growth. Only a few studies have investigated the mechanism underlying the transcriptional-level response of Morella cerifera to saline-alkali stress. Based on RNA-seq technology, gene e...
(1) Background: Sepsis is present in nearly 90% of critically ill patients with community-acquired pneumonia (CAP). This systematic review updates the information on studies that have assessed gene expression profiles in critically ill septic patient...
The growing volume and complexity of gene expression data necessitate biologically meaningful and statistically robust methods for feature selection to enhance the effectiveness of disease diagnosis systems. The present study addresses this challenge...
Ulcerative colitis (UC) arises from a complex interplay between host and environmental factors, but with a largely unsolved pathophysiology. The pathophysiology was outlined by RNA-sequencing of mucosal biopsies from non-inflamed and inflamed colon o...
Statistical methods for enrichment analysis are important tools to extract biological information from omics experiments. Although these methods have been widely used for the analysis of gene and protein lists, the development of high-throughput tech...
Glioblastoma multiforme (GBM) is categorized by rapid malignant cellular growth in the central nervous system (CNS) tumors. It is one of the most prevailing primary brain tumors, particularly in human male adults. Even though the combination therapy...
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