Neighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical...
I argue that mental health is not a property of individual minds but emerges in the shared space between embodied beings. Drawing on Dōgen’s account of unbroken continuity, I propose that interbodily mental health depends on cultivating ma...
Transcriptomics has significantly grown as a functional genomics tool for understanding the expression of biological systems. The generated transcriptomics data can be utilised to produce a gene co-expression network that is one of the essential down...
Breast cancer is a heterogeneous disease comprising various subtypes with distinct molecular characteristics, clinical outcomes, and therapeutic responses. This heterogeneity evidences significant challenges for diagnosis, prognosis, and treatment. T...
Rhabdomyosarcoma is subclassified by the presence or absence of a recurrent chromosome translocation that fuses the FOXO1 and PAX3 or PAX7 genes. The fusion protein (FOXO1-PAX3/7) retains both binding domains and becomes a novel and potent transcript...
Breast cancer is a complex phenotype (or better yet, several complex phenotypes) characterized by the interplay of a large number of cellular and biomolecular entities. Biological networks have been successfully used to capture some of the heterogene...
A highly potent antitoxin for botulinum neurotoxin (BoNT) serotypes A and B has been developed that comprises three monoclonal antibodies (mAbs) targeting BoNT/A and three targeting BoNT/B. These oligoclonal antibody combinations neutralize toxin by...
To identify sets of genes that exhibit similar expression characteristics, co-expression networks were constructed from transcriptome datasets that were obtained from plant samples at various stages of growth and development or treated with diverse b...
Metabolic reprogramming is a hallmark of cancer. Such reprogramming entails the up-regulation of the expression of specific mitochondrial proteins, thus increasing the burden on the mitochondrial protein quality control. However, very little is known...
WUSCHEL-related homeobox (WOX) genes are a class of plant-specific transcription factors, regulating the development of multiple tissues. However, the genomic characterizations and expression patterns of WOX genes have not been analyzed in lotus. In...
Plant height (PH) is a vital agronomic trait that significantly affects cotton yield and facilitates mechanized harvesting. Gaining insights into the genetic regulatory mechanisms governing plant height is fundamental to advancing cotton breeding. In...
Network-based systems biology has become an important method for analyzing high-throughput gene expression data and gene function mining. Escherichia coli (E. coli) has long been a popular model organism for basic biological research. In this paper,...
Among biological networks, co-expression networks have been widely studied. One of the most commonly used pipelines for the construction of co-expression networks is weighted gene co-expression network analysis (WGCNA), which can identify highly co-e...
Breast cancer encompasses a diverse array of subtypes, each exhibiting distinct clinical characteristics and treatment responses. Unraveling the underlying regulatory mechanisms that govern gene expression patterns in these subtypes is essential for...
The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD)....
Bacteriophage ΦIN93 has an icosahedral-like capsid that is believed to be composed of two putative capsid or coat proteins, namely open reading frame (ORF)13 and ORF14. In addition to the two capsid proteins, there are other proteins that may be...
Gene co-expression network analysis has been widely used in gene function annotation, especially for long noncoding RNAs (lncRNAs). However, there is a lack of effective cross-platform analysis tools. For biologists to easily build a gene co-expressi...
The coding region for the sortase A (SrtA) of Staphylococcus aureus was fused at the N-terminus of LfcinB. The SrtA-LfcinB fusion protein in E. coli C43(DE3) was expressed with the expected sizes of 21 kDa and 38 kDa by pET21b-SrtA-LfcinB and pET32-1...
Bombyx mori is an important economic insect and an animal model in pharmacomedical research. Although its physiology has been studied for many years, the mechanism via which silk protein genes are regulated remains unclear. In this study, we performe...
Colorectal cancer (CRC) is driven in part by dysregulated Wnt, Ras-Raf-MAPK, TGF-β, and PI3K-Akt signaling. The progression of CRC is also promoted by molecular alterations and heterogeneous—yet interconnected—gene mutations, chromos...
The underlying mechanisms of eating disorders (EDs) are very complicated and still poorly understood. The pathogenesis of EDs may involve the interplay of multiple genes. To investigate the dysregulated gene pathways in EDs we analyzed gene expressio...
Introduction: Tumor necrosis factor (TNFα) is an important proinflammatory cytokine in rheumatoid arthritis (RA) immune processes. However, TNFα activity and functions may be regulated by soluble receptors, which act as decoys, and by num...
Biological systems respond to perturbations through the rewiring of molecular interactions, organised in gene regulatory networks (GRNs). Among these, the increasingly high availability of transcriptomic data makes gene co-expression networks the mos...
Inference of co-expression network and identification of disease-related modules and gene sets can help us understand disease-related molecular pathophysiology. We aimed to identify a cardiovascular disease (CVD)-related transcriptomic signature, spe...
Subtilases (SBTs), which belong to the serine peptidases, control plant development by regulating cell wall properties and the activity of extracellular signaling molecules, and affect all stages of the life cycle, such as seed development and germin...
(1) Differential co-expression analysis between two phenotypes with a known gene set helps to uncover gene regulation alterations. (2) GSNCASCR uses CSCORE to estimate the gene pair correlations for network reconstruction and GSNCA to quantify the st...
Caenorhabditis elegans (C. elegans) is a well-characterized metazoan, whose transcriptome has been profiled in different tissues, development stages, or other conditions. Large-scale transcriptomes can be reused for gene function annotation through s...
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)...
Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prior...
An 8-year-old female neutered Labrador retriever was presented for a second opinion consultation due to vomiting and lethargy, having failed to respond to symptomatic therapy. Blood analysis revealed hyperbilirubinemia and hypoalbuminemia, associated...
Promising efforts are ongoing to extend genomics resources for pikeperch (Sander lucioperca), a species of high interest for the sustainable European aquaculture sector. Although previous work, including reference genome assembly, transcriptome seque...
Autophagy is involved in the development and differentiation of many cell types. It is essential for the pre-adipocytes to respond to the differentiation stimuli and may contribute to reorganizing the intracellulum to adapt the morphological and meta...
Long non–coding RNAs (lncRNAs) are emerging as key gene regulators in the pathogenesis and development of various cancers including B lymphoblastic leukaemia (B–ALL). In this pilot study, we used RNA–Seq transcriptomic data for iden...
Long non-coding RNAs (lncRNAs) are functional transcripts with more than 200 nucleotides. These molecules exhibit great regulatory capacity and may act at different levels of gene expression regulation. Despite this regulatory versatility, the biolog...
Background: Malaria results in more than 550,000 deaths each year due to drug resistance in the most lethal Plasmodium (P.) species P. falciparum. A full P. falciparum genome was published in 2002, yet 44.6% of its genes have unknown functions. Impro...
Transient receptor potential (TRP) ankyrin 1 (TRPA1) and vanilloid 1 (TRPV1) receptors are implicated in modulation of cough and nociception. In vivo, TRPA1 and TRPV1 are often co-expressed in neurons and TRPA1V1 hetero-tetramer formation is noted in...
Previous studies have identified numerous transcription factors involved in drought response, each of which play different roles in plants. The objective of the present study was to evaluate the effectiveness of two transcription factors on drought r...
Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (...
Background/Objectives: Waxy corn has a unique taste and flavor that a majority of consumers love, and the market application prospect is broad. Nitrogen plays an important role in the growth and development of waxy corn. Exploring the key genes that...
High-throughput sequencing technologies have enabled the generation of single-cell RNA-seq (scRNA-seq) data, which explore both genetic heterogeneity and phenotypic variation between cells. Some methods have been proposed to detect the related genes...
Microarray techniques are used to generate a large amount of information on gene expression. This information can be statistically processed and analyzed to identify the genes useful for the diagnosis and prognosis of genetic diseases. Game theoretic...
Skin cutaneous melanoma (SCM) is a common malignant tumor of the skin and its pathogenesis still needs to be studied. In this work, we constructed a co-expression network and screened for hub genes by weighted gene co-expression network analysis (WGC...
MicroRNAs (miRNAs) have been proposed as promising biomarkers for periodontal disease because of their role in regulating inflammation and tissue remodeling. This study evaluated the salivary expressions of miR-34a, miR-155, and miR-146a and their re...
Feather follicle density plays an important role in appealing to consumers’ first impressions when making purchasing decisions. However, the molecular network that contributes to this trait remains largely unknown. The aim of this study was to...
Deep RNA sequencing of 164 blood samples collected from long-lived families was performed to investigate the expression patterns of circular RNAs (circRNAs). Unlike that observed in previous studies, circRNA expression in long-lived elderly individua...
With the development of society, the incidence of dementia and type 2 diabetes (T2DM) in the elderly has been increasing. Although the correlation between T2DM and mild cognitive impairment (MCI) has been confirmed in the previous literature, the int...
In order to develop an effective and safe immunomodulator to enhance the antimicrobial bioactivity and immunity of animals against infectious bacterial diseases, a recombinant plasmid pGAPZαA-IL2-B co-expressing pig interleukin-2 (PIL-2) and fu...
The rising prevalence of Alzheimer’s disease (AD), particularly among older adults, has driven increased research into its underlying mechanisms and risk factors. Aging, genetic susceptibility, and cardiovascular health are recognized contribut...
Gene Networks (GN), have emerged as an useful tool in recent years for the analysis of different diseases in the field of biomedicine. In particular, GNs have been widely applied for the study and analysis of different types of cancer. In this contex...
Human fibroblast growth factor 19 (hFGF19) is a difficult-to-express protein that is frequently fused with another protein for soluble expression. However, residual amino acids after cleavage with protease represent one of the major problems in thera...
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