1,813 Results Found

Breast cancer metastasis can have a fatal outcome, with the prediction of metastasis being critical for establishing effective treatment strategies. RNA-sequencing (RNA-seq) is a good tool for identifying genes that promote and support metastasis dev...

The gene expression profile has the characteristics of a high dimension, low sample, and continuous type, and it is a great challenge to use gene expression profile data for the classification of tumor samples. This paper proposes a cross-entropy bas...

One of the current focuses of modern bioinformatics is the development of hybrid models to process gene expression data, in order to create diagnostic systems for various diseases. In this study, we propose a solution to this problem that combines an...

Background: Breast cancer (BC) is one of the most common female cancers. Clinical and histopathological information is collectively used for diagnosis, but is often not precise. We applied machine learning (ML) methods to identify the valuable gene s...

The rapid growth of diverse $\text{-}\mathrm{omics}$ datasets has made multiomics data integration crucial in cancer research. This study adapts the expectation–maximization routine for the joint latent variable modeling of multiomics patient profiles. By combin...

In this paper, we present the results of the research concerning extraction of informative gene expression profiles from high-dimensional array of gene expressions considering the state of patients’ health using clustering method, ML-based bina...

Induced pluripotent stem cells (iPSCs) are pluripotent cells derived from adult somatic cells. After the pioneering work by Yamanaka, who first generated iPSCs by retroviral transduction of four reprogramming factors, several alternative methods to o...

Gene co-expression networks are powerful tools to understand functional interactions between genes. However, large co-expression networks are difficult to interpret and do not guarantee that the relations found will be true for different genotypes. S...

Due to the diverse medicinal effects, polyphenols are among the most intensively studied natural products. However, it is a great challenge to elucidate the polypharmacological mechanisms of polyphenols. To address this challenge, we establish a meth...

(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...

Using RNA-seq digital difference expression profiling methods, we have assessed the gene expression profiles of hemocytes harvested from Heliothis virescens that were challenged with Helicoverpa zea single nucleopolyhedrovirus (HzSNPV). A reference t...

In the field of gene expression analysis, methods of integrating multiple gene expression profiles are still being developed and the existing methods have scope for improvement. The previously proposed tensor decomposition-based unsupervised feature...

It is believed that caspases may play a significant role in the development of cancer, and the expression levels of genes encoding these proteins may influence the prognosis and clinical course of cancer. Taking into account the information presented...

Hepatitis E is a liver inflammation caused by infection with the hepatitis E virus (HEV). Every year, there are an estimated 20 million HEV infections worldwide, leading to an estimated 3.3 million symptomatic cases of hepatitis E. HEV viral load has...

Background: This study aimed to perform a comprehensive gene expression analysis in patients with early-stage gastric cancer (EGC) to identify gene expression profiles specific to gastric cancer (GC) lesions. Methods: Biopsy specimens were collected...

Objectives: Technological advances in identifying gene expression profiles are being applied to study an array of cancers. The goal of this study was to identify differentially expressed genes in pancreatic ductal adenocarcinoma (PDAC) and examine th...

Background: Hepatocellular carcinoma (HCC) is a major threat to public health. However, few effective therapeutic strategies exist. We aimed to identify potentially therapeutic target genes of HCC by analyzing three gene expression profiles. Methods:...

As a common brain cancer derived from glial cells, gliomas have three subtypes: glioblastoma, diffuse astrocytoma, and anaplastic astrocytoma. The subtypes have distinctive clinical features but are closely related to each other. A glioblastoma can b...

(1) Background: Emergence of methods interrogating gene expression at high throughput gave birth to quantitative transcriptomics, but also posed a question of inter-comparison of expression profiles obtained using different equipment and protocols an...

Natural medicines have attracted wide attention in recent years. It is of great significance to clarify the pharmacological mechanisms of natural medicines. In prior studies, we established a method for elucidating pharmacological mechanisms of natur...

Background: Gene expression signatures correlate genetic alterations with specific clinical features, providing the potential for clinical usage. A plethora of HCC-dependent gene signatures have been developed in the last two decades. However, none o...

Background/Objectives: Leeches constitute a pharmacologically significant animal group in traditional medicine due to their antithrombotic peptides, which include numerous members of the hirustasin gene superfamily. However, a comparative expression...

Aims: The diagnostic approach to idiopathic giant-cell myocarditis (IGCM) is based on identifying various patterns of inflammatory cell infiltration and multinucleated giant cells (GCs) in histologic sections taken from endomyocardial biopsies (EMBs)...

Background: Oral squamous cell carcinoma (OSCC) is one of the most commonly detected neoplasms worldwide. Not all mechanisms associated with cell cycle disturbances are known in OSCC. Examples of genes involved in the control of the cell cycle are CD...

The DKK family is a canonical small family of WNT antagonists. Though recent studies have suggested that the DKK gene family may be involved in sex differentiation in Pelodiscus sinensis, there are still a lot of things about the DKK gene family that...

In this paper, we present a comparative analysis of the transcriptomic profile of three different human cell types: hematopoietic stem cells (HSCs), bone marrow-derived mesenchymal stem cells (MSCs) and fibroblasts (FIBs). The work aims to identify u...

Recent advances in preimplantation embryo diagnostics enable a wide range of applications using single cell biopsy and molecular-based selection techniques without compromising embryo production. This study was conducted to develop a single cell embr...

Gene expression analysis is crucial in understanding cellular processes, development, health, and disease. With RNA-seq outpacing microarray as the chosen platform for gene expression, is there space for array data in future profiling? This study inv...

Background and Objectives: Breast cancer is a heterogeneous disease categorized into four subtypes. Previous studies have shown that copy number alterations of several genes are implicated with the development and progression of many cancers. This st...

Gene expression profiling is one of the most reliable high-throughput phenotyping methods, allowing researchers to quantify the transcript abundance of expressed genes. Because many biotic and abiotic factors influence gene expression, it is recommen...

Background and aim: Resistance to chemotherapy is the key obstacle to the effective treat- ment of various cancers. Accumulating evidence suggests significant involvement of the epithelial-to-mesenchymal transition (EMT) in the chemoresistance of mos...

Discovering a genetic regulatory network (GRN) from time series gene expression data plays an essential role in the field of biomedical research. In its development, many methods have been proposed for inferring GRNs. Although most of them are effect...

Background: Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by immune dysregulation and chronic inflammation across various organ systems. While anti-dsDNA and anti-Sm antibodies are commonly associated with SLE, the presen...

The problems of gene regulatory network (GRN) reconstruction and the creation of disease diagnostic effective systems based on genes expression data are some of the current directions of modern bioinformatics. In this manuscript, we present the resul...

Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by e...

Background/Objectives: The African swine fever virus (ASFV) multi-gene family (MGF) 360 proteins play critical roles in immune evasion, replication regulation, and virulence determination. Despite substantial advances in this field, the functional ro...

Background/Objectives: The translation of in vitro biomaterial evaluations into successful clinical applications often fails due to discrepancies with in vivo results. Previously, we demonstrated that differences in culture medium conditions influenc...

Background and objectives: Mutational analysis has led to a better understanding of acute myeloid leukemia (AML) biology and to an improvement in clinical management. Some of the most important mutations that affect AML biology are represented by mut...

Background/Objectives: Despite current treatments extending the lifespan of Glioblastoma (GBM) patients, the average survival time is around 15–18 months, underscoring the fatality of GBM. This study aims to investigate the impact of sample het...

Background: The prognostic impact of the expression profile of genes recurrently amplified in glioblastoma multiforme (GBM) remains controversial. Methods: We investigated the RNA gene expression profile of epidermal growth factor receptor (EGFR), cy...

The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) plays an important role in plant nitrate absorption, distribution, and nitrogen use efficiency. Nevertheless, few reports are available regarding Eucalyptus grandis NPF genes...

A comprehensive gene expression investigation requires high-quality RNA extraction, in sufficient amounts for real-time quantitative polymerase chain reaction and next-generation sequencing. In this work, we compared different RNA extraction methods...

The development of the medical applications for substances or materials that contact cells is important. Hence, it is necessary to elucidate how substances that surround cells affect gene expression during incubation. In the current study, we compare...

Xanthomonas phaseoli pv. dieffenbachiae (Xpd), the causal agent of bacterial blight in Anthurium within the Araceae family, is listed as an EPPO A2 quarantine organism. Although the whole genome of Xpd has been sequenced, the molecular mechanisms und...

The European honey bee is a model organism for studying social behaviors. Comprehensive analyses focusing on the differential expression profiles of genes between the brains of nurse bees and foragers, or in the mushroom bodies—the brain struct...

The relationship between gene expression profiles and cellular phenotypes is an important aspect of functional genomics. Clinical tissue specimens will play a vital role in this effort. The usefulness of tissue for molecular profiling is significantl...

Mutations are heritable changes at the base level of genomic DNA. Furthermore, mutations lead to genetic polymorphisms and may alter animal growth phenotypes. Our previous study found that mutations in the bovine Actin-like protein 8 (ACTL8) gene may...

(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...

Background. Infantile hemangiomas may have unexpected behavior. Initial regression (spontaneously or drug-induced) may be followed by unexplained recurrences. At this moment, there are no well-established criteria to predict infantile hemangioma recc...

Gene expression-based tumor classification aims to distinguish tumor types based on gene expression profiles. This task is difficult due to the high dimensionality of gene expression data and limited sample sizes. Most datasets contain tens of thousa...