28,800 results match your criteria gene ontology


Bioinformatics analysis of sequential gene expression profiling after skin and skeletal muscle wound in mice.

Leg Med (Tokyo) 2021 Oct 19;54:101982. Epub 2021 Oct 19.

School of Forensic Medicine, Henan University of Science and Technology, Luoyang 471003, China. Electronic address:

It is of great value to use bioinformatics methods to screen the core differentially expressed genes (DEGs) at different times after mouse skin and skeletal muscle wound, and to explore the relationship between them and the wound age. To this end, we downloaded the gene expression profiles of GSE140517 and GSE23006 from the NCBI-GEO gene database, used GEO2R online tools and Venn diagrams to screen out DEGs at different times and common-DEGs. The Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) channel analysis were carried out through the DAVID website respectively. Read More

View Article and Full-Text PDF
October 2021

Molecular response mechanisms of silkworm (Bombyx mori L.) to the toxicity of 1-octyl-3-methylimidazole chloride based on transcriptome analysis of midguts and silk glands.

Ecotoxicol Environ Saf 2021 Oct 20;227:112915. Epub 2021 Oct 20.

College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, People's Republic of China. Electronic address:

In a previous study, silkworm larvae were used as a novel model to assess the biotoxicity of ILs, which showed that ILs could cause significant physiological and biochemical changes in midguts and silk glands of the larvae, and result in the death of larvae. In order to investigate the toxicity of 1-octyl-3-methylimidazole chloride ([Cmim]Cl) to the larvae at molecular level, RNA-sequencing technology was used to construct transcriptomic profiles of midguts and silk glands in this work. Results showed that a lot of differentially expressed genes (DEGs) were effectively screened out through bioinformatics software based on the transcriptome data and reference genome. Read More

View Article and Full-Text PDF
October 2021

Altered gene expression in slc4a11 mouse cornea highlights SLC4A11 roles.

Sci Rep 2021 Oct 22;11(1):20885. Epub 2021 Oct 22.

Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, T6G 2H7, Canada.

SLC4A11 is a H/NH/water transport protein, of corneal endothelial cells. SLC4A11 mutations cause congenital hereditary endothelial dystrophy and some cases of Fuchs endothelial corneal dystrophy. To probe SLC4A11's roles, we compared gene expression in RNA from corneas of 17-week-old slc4a11 (n = 3) and slc4a11 mice (n = 3) and subjected to RNA sequencing. Read More

View Article and Full-Text PDF
October 2021

Selected ideal natural ligand against TNBC by inhibiting CDC20, using bioinformatics and molecular biology.

Aging (Albany NY) 2021 Oct 22;13(undefined). Epub 2021 Oct 22.

Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China.

Object: Find potential therapeutic targets of triple-negative breast cancer (TNBC) patients by bioinformatics. Screen ideal natural ligand that can bind with the potential target and inhibit it by using molecular biology.

Methods: Bioinformatics and molecular biology were combined to analyze potential therapeutic targets. Read More

View Article and Full-Text PDF
October 2021

Upregulation of cathepsin L gene under mild cold conditions in young Japanese male adults.

J Physiol Anthropol 2021 Oct 22;40(1):16. Epub 2021 Oct 22.

Department of Human Science, Faculty of Design, Kyushu University, 4-9-1 Shiobaru, Minami-ku, Fukuoka, 815-8540, Japan.

Background: Physiological thermoregulatory systems in humans have been a key factor for adaptation to local environments after their exodus from Africa, particularly, to cold environments outside Africa. Recent studies using high-throughput sequencing have identified various genes responsible for cold adaptation. However, the molecular mechanisms underlying initial thermoregulation in response to acute cold exposure remain unclear. Read More

View Article and Full-Text PDF
October 2021

Microarray profile analysis identifies ETS1 as potential biomarker regulated by miR-23b and modulates TCF4 in gastric cancer.

World J Surg Oncol 2021 Oct 23;19(1):311. Epub 2021 Oct 23.

The Department of Oncology, Beijing Mentougou District Hospital, Beijing, 102300, People's Republic of China.

Background: Gastric cancer (GC), a common malignancy of the human digestive system, represents the second leading cause of cancer-related deaths worldwide. Early detection of GC has a significant impact on clinical outcomes. The aim of this study was to identify potential GC biomarkers. Read More

View Article and Full-Text PDF
October 2021

Microarray Analysis of Paramylon, Isolated from Euglena Gracilis EOD-1, and Its Effects on Lipid Metabolism in the Ileum and Liver in Diet-Induced Obese Mice.

Nutrients 2021 Sep 27;13(10). Epub 2021 Sep 27.

Studies in Human Life Sciences, Graduate School of Studies in Human Culture, Otsuma Women's University, Chiyoda-ku, Tokyo 102-8357, Japan.

We previously showed that supplementation of a high fat diet with paramylon (PM) reduces the postprandial glucose rise, serum total and LDL cholesterol levels, and abdominal fat accumulation in mice. The purpose of this study was to explore the underlying mechanism of PM using microarray analysis. Male mice (C57BL/BL strain) were fed an experimental diet (50% fat energy) containing 5% PM isolated from EOD-1 for 12 weeks. Read More

View Article and Full-Text PDF
September 2021

Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection.

J Fungi (Basel) 2021 Oct 14;7(10). Epub 2021 Oct 14.

Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary.

Fission yeasts have a unique life history and exhibit distinct evolutionary patterns from other yeasts. Besides, the species demonstrate stable genome structures despite the relatively fast evolution of their genomic sequences. To reveal what could be the reason for that, comparative genomic analyses were carried out. Read More

View Article and Full-Text PDF
October 2021

Entropy-Based Graph Clustering of PPI Networks for Predicting Overlapping Functional Modules of Proteins.

Entropy (Basel) 2021 Sep 28;23(10). Epub 2021 Sep 28.

Division of Software, Yonsei University Mirae Campus, Wonju-si 26493, Gangwon-do, Korea.

Functional modules can be predicted using genome-wide protein-protein interactions (PPIs) from a systematic perspective. Various graph clustering algorithms have been applied to PPI networks for this task. In particular, the detection of overlapping clusters is necessary because a protein is involved in multiple functions under different conditions. Read More

View Article and Full-Text PDF
September 2021

Global Proteomic Analysis of Response to Linalool.

Foods 2021 Oct 14;10(10). Epub 2021 Oct 14.

Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.

(LM) is one of the most serious foodborne pathogens. Listeriosis, the disease caused by LM infection, has drawn attention worldwide because of its high hospitalization and mortality rates. Linalool is a vital constituent found in many essential oils; our previous studies have proved that linalool exhibits strong anti- activity. Read More

View Article and Full-Text PDF
October 2021

Deep Modeling of Regulating Effects of Small Molecules on Longevity-Associated Genes.

Pharmaceuticals (Basel) 2021 Sep 22;14(10). Epub 2021 Sep 22.

Vancouver Prostate Centre, Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3Z6, Canada.

Aging is considered an inevitable process that causes deleterious effects in the functioning and appearance of cells, tissues, and organs. Recent emergence of large-scale gene expression datasets and significant advances in machine learning techniques have enabled drug repurposing efforts in promoting longevity. In this work, we further developed our previous approach-DeepCOP, a quantitative chemogenomic model that predicts gene regulating effects, and extended its application across multiple cell lines presented in LINCS to predict aging gene regulating effects induced by small molecules. Read More

View Article and Full-Text PDF
September 2021

Assembly and Analysis of Tissue-Specific Transcriptomes of the Edible Red Sea Urchin Using RNA-Seq.

Biology (Basel) 2021 Oct 2;10(10). Epub 2021 Oct 2.

Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile.

Edible red sea urchin () is an endemic echinoderm species of the Chilean coasts. The worldwide demand for high-quality gonads of this species has addressed the depletion of its natural populations. Studies on this sea urchin are limited, and genomic information is almost nonexistent. Read More

View Article and Full-Text PDF
October 2021

Identification of Five Hub Genes as Key Prognostic Biomarkers in Liver Cancer via Integrated Bioinformatics Analysis.

Biology (Basel) 2021 Sep 24;10(10). Epub 2021 Sep 24.

Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam.

Liver cancer is one of the most common cancers and the top leading cause of cancer death globally. However, the molecular mechanisms of liver tumorigenesis and progression remain unclear. In the current study, we investigated the hub genes and the potential molecular pathways through which these genes contribute to liver cancer onset and development. Read More

View Article and Full-Text PDF
September 2021

Single-Cell RNA-Seq Revealed the Gene Expression Pattern during the In Vitro Maturation of Donkey Oocytes.

Genes (Basel) 2021 Oct 19;12(10). Epub 2021 Oct 19.

Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Univesity, Nanning 530005, China.

Donkeys are an important domesticated animal, providing labor, meat, milk, and medicinal materials for humans. However, the donkey population is continuously declining and even at risk of extinction. The application of modern animal production technology, such as oocyte in vitro maturation, is a promising method to improve the donkey population. Read More

View Article and Full-Text PDF
October 2021

Novel Candidate Genes Differentially Expressed in Glyphosate-Treated Horseweed ().

Genes (Basel) 2021 Oct 14;12(10). Epub 2021 Oct 14.

Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA.

The evolution of herbicide-resistant weed species is a serious threat for weed control. Therefore, we need an improved understanding of how gene regulation confers herbicide resistance in order to slow the evolution of resistance. The present study analyzed differentially expressed genes after glyphosate treatment on a glyphosate-resistant Tennessee ecotype (TNR) of horseweed (), compared to a susceptible biotype (TNS). Read More

View Article and Full-Text PDF
October 2021

Comparative RNA-Seq Analyses of (Hymenoptera: Formicidae) Reveal Gene in Response to Cold Stress.

Genes (Basel) 2021 Oct 13;12(10). Epub 2021 Oct 13.

Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea.

, as a fire ant species, shows some predatory behavior towards earthworms and woodlice, and preys on the larvae of other ant species by tunneling into a neighboring colony's brood chamber. This study focused on the molecular response process and gene expression profiles of to low (9 °C)-temperature stress in comparison with normal temperature (25 °C) conditions. A total of 89,657 unigenes (the clustered non-redundant transcripts that are filtered from the longest assembled contigs) were obtained, of which 32,782 were annotated in the NR (nonredundant protein) database with gene ontology (GO) terms, gene descriptions, and metabolic pathways. Read More

View Article and Full-Text PDF
October 2021

Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete .

Genes (Basel) 2021 Sep 29;12(10). Epub 2021 Sep 29.

Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.

A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome of has been reported previously, but it is essentially limited to open reading frames (ORFs) of protein coding genes and contains only a few noncoding transcripts. In this study, we identified and annotated full-length transcripts of by deep RNA sequencing. Read More

View Article and Full-Text PDF
September 2021

The Transcriptomic Landscape of Molecular Effects after Sublethal Exposure to Dinotefuran on .

Insects 2021 Oct 2;12(10). Epub 2021 Oct 2.

College of Animal Sciences, Shanxi Agricultural University, Taigu 030801, China.

The decreasing number of bees is a global ecological problem. With the advancement of agricultural modernisation, the large-scale use of neonicotinoid insecticides is one of the main factors leading to the decline of bees. The aim of the present study was to investigate the effect and the mechanisms underlying bees impaired by dinotefuran. Read More

View Article and Full-Text PDF
October 2021

Characterization of Proteins Regulated by Androgen and Protein Kinase a Signaling in VCaP Prostate Cancer Cells.

Biomedicines 2021 Oct 6;9(10). Epub 2021 Oct 6.

Department of Cancer Biomedical Science, National Cancer Center-Graduate School of Cancer Science and Policy, 323 Ilsan-ro, Ilsandong-gu, Goyang-si 10408, Korea.

Androgen signaling via the androgen receptor (AR) is involved in normal prostate development and prostate cancer progression. In addition to androgen binding, a variety of protein kinases, including cyclic AMP-dependent protein kinase A (PKA), can activate the AR. Although hormone deprivation, especially that of androgen, continues to be an important strategy for treating prostate cancer patients, the disease ultimately progresses to castration-resistant prostate cancer (CRPC), despite a continuous hormone-deprived environment. Read More

View Article and Full-Text PDF
October 2021

Transcriptional Profiling of Tumorspheres Reveals TRPM4 as a Novel Stemness Regulator in Breast Cancer.

Biomedicines 2021 Oct 1;9(10). Epub 2021 Oct 1.

Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology, 45110 Ioannina, Greece.

Cancer stem cells (CSCs) have been implicated in the development of chemoresistance, tumor recurrence and metastasis in breast cancer, thus emerging as a promising target for novel therapies. To identify novel stemness regulators that could potentially be targeted in luminal ER tumors, we performed RNA-sequencing (RNA-seq) in MCF-7 adherent monolayer cells and tumorspheres enriched in breast CSCs (bCSCs). We identified 1421 differentially expressed genes (DEGs), with 923 of them being upregulated and 498 downregulated in tumorspheres. Read More

View Article and Full-Text PDF
October 2021

A Systems Approach to Interrogate Gene Expression Patterns in African American Men Presenting with Clinically Localized Prostate Cancer.

Cancers (Basel) 2021 Oct 14;13(20). Epub 2021 Oct 14.

Hollings Cancer Center, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA.

An emerging theory about racial differences in cancer risk and outcomes is that psychological and social stressors influence cellular stress responses; however, limited empirical data are available on racial differences in cellular stress responses among men who are at risk for adverse prostate cancer outcomes. In this study, we undertook a systems approach to examine molecular profiles and cellular stress responses in an important segment of African American (AA) and European American (EA) men: men undergoing prostate biopsy. We assessed the prostate transcriptome with a single biopsy core via high throughput RNA sequencing (RNA-Seq). Read More

View Article and Full-Text PDF
October 2021

Genome-Wide Transcriptome Profiling, Characterization, and Functional Identification of Transcription Factors in Sorghum under Salt Stress.

Antioxidants (Basel) 2021 Oct 13;10(10). Epub 2021 Oct 13.

Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.

Salinity stress has become a significant concern to global food security. Revealing the mechanisms that enable plants to survive under salinity has immense significance. Sorghum has increasingly attracted researchers interested in understanding the survival and adaptation strategies to high salinity. Read More

View Article and Full-Text PDF
October 2021

Identification of a Somatic Mutation-Derived Long Non-Coding RNA Signatures of Genomic Instability in Renal Cell Carcinoma.

Front Oncol 2021 5;11:728181. Epub 2021 Oct 5.

Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China.

Background: Renal cell carcinoma (RCC) is a malignant tumor with high morbidity and mortality. It is characterized by a large number of somatic mutations and genomic instability. Long non-coding RNAs (lncRNAs) are widely involved in the expression of genomic instability in renal cell carcinoma. Read More

View Article and Full-Text PDF
October 2021

Prognostic Signatures of Alternative Splicing Events in Esophageal Carcinoma Based on TCGA Splice-Seq Data.

Front Oncol 2021 5;11:658262. Epub 2021 Oct 5.

Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.

An alternative splicing (AS) event is a highly complex process that plays an essential role in post-transcriptional gene expression. Several studies have suggested that abnormal AS events were the primary element in the pathological process of cancer. However, few works are dedicated to the study of AS events in esophageal carcinoma (EC). Read More

View Article and Full-Text PDF
October 2021

UHRF1 Could Be a Prognostic Biomarker and Correlated with Immune Cell Infiltration in Hepatocellular Carcinoma.

Int J Gen Med 2021 13;14:6769-6776. Epub 2021 Oct 13.

Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, People's Republic of China.

Objective: This study was performed to investigate the relationship among UHRF1 expression, its biological function and immune infiltration in human hepatocellular carcinoma (HCC).

Methods: Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine, and The Cancer Genome Atlas (TCGA) databases were used to analyze UHRF1 expression between HCC and normal tissues. Subsequently, GEPIA, TCGA-Portal, Kaplan-Meier Plotter, Protein Atlas and SurvExpress databases were utilized for survival analysis. Read More

View Article and Full-Text PDF
October 2021

Construction of a New Tumor Immunity-Related Signature to Assess and Classify the Prognostic Risk of Colorectal Cancer.

Int J Gen Med 2021 12;14:6661-6676. Epub 2021 Oct 12.

Department of Gastroenterology, Changxing People's Hospital, Huzhou City, People's Republic of China.

Purpose: Although immunotherapy and checkpoint inhibitors contribute to the treatment of colorectal cancer (CRC), few patients can benefit from these treatments. Therefore, our goal was to develop a marker based on immune-related genes to predict the prognosis of patients with CRC to guide treatment strategies.

Methods: Gene expression data from colorectal cancer patients in the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas were analyzed systematically. Read More

View Article and Full-Text PDF
October 2021

Construction and Investigation of Competing Endogenous RNA Networks and Candidate Genes Involved in SARS-CoV-2 Infection.

Int J Gen Med 2021 12;14:6647-6659. Epub 2021 Oct 12.

Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, People's Republic of China.

Introduction: The current COVID-19 pandemic caused by a novel coronavirus SARS-CoV-2 is a quickly developing global health crisis, yet the mechanisms of pathogenesis in COVID-19 are not fully understood.

Methods: The RNA sequencing data of SARS-CoV-2-infected cells was obtained from the Gene Expression Omnibus (GEO). The differentially expressed mRNAs (DEmRNAs), long non-coding RNAs (DElncRNAs), and microRNAs (DEmiRNAs) were identified by edgeR, and the SARS-CoV-2-associated competing endogenous RNA (ceRNA) network was constructed based on the prediction of bioinformatic databases. Read More

View Article and Full-Text PDF
October 2021

An Autophagy-Related Long Non-Coding RNA Prognostic Signature for Patients with Lung Squamous Carcinoma Based on Bioinformatics Analysis.

Int J Gen Med 2021 12;14:6621-6637. Epub 2021 Oct 12.

Department of Critical Care and Respiratory Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China.

Purpose: Lung cancer is the most common and deadly cancer type affecting humans. Although huge progress has been made on early diagnosis and precision treatment, the overall 5 year survival rate remains low. In this study, we constructed an autophagy-related long non-coding RNA (lncRNA) prognostic signature for guiding clinical practice. Read More

View Article and Full-Text PDF
October 2021

A network pharmacological approach to reveal the multidrug resistance reversal and associated mechanisms of acetogenins against colorectal cancer.

J Biomol Struct Dyn 2021 Oct 20:1-20. Epub 2021 Oct 20.

Department of Biotechnology, PSG College of Technology, Coimbatore, Tamil Nadu, India.

Multidrug Resistance (MDR) in tumors is caused by the over-expression of ATP Binding Cassette transporter proteins such as Multidrug Resistance Protein 1 and Breast Cancer Resistance Protein 1. This study focuses on identifying a MDR inhibitor among acetogenins (AGEs) of and also aims at predicting colorectal cancer (CRC) core targets of AGEs through a network pharmacological approach. Twenty-four AGEs were initially screened for their ADME properties. Read More

View Article and Full-Text PDF
October 2021

Transcriptomic landscape of gene expression profiles and pathways in JORRP tumor tissues and HPV6/11 E6-E7-overexpressing HNSCC cell lines.

J Virol 2021 Oct 20:JVI0134221. Epub 2021 Oct 20.

Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China.

Juvenile-onset recurrent respiratory papillomatosis (JORRP) is the most common benign laryngeal neoplasm in children and is considered to be primarily caused by human papillomavirus (HPV) types 6 and 11. In the present study, we performed RNA sequencing (RNA-seq) of 8 tumors and 4 adjacent nontumor tissues to explore the transcriptional profiles of JORRP tumors. A total of 1151 upregulated genes involved in the IL-17 signaling pathway and 1620 downregulated genes involved in dysregulated inflammatory responses were reported. Read More

View Article and Full-Text PDF
October 2021