68,881 results match your criteria enrichment analysis


Use of transcriptomic analysis to identify microRNAs related to the effect of stress on thymus immune function in a chicken stress model.

Res Vet Sci 2021 Sep 10;140:233-241. Epub 2021 Sep 10.

College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China. Electronic address:

In modern poultry production, stress-induced immunosuppression leads to serious economic losses and harm to animals, but the molecular mechanisms governing the effects of stress on the chicken thymus have not been elucidated. In this study, we successfully constructed a stress model of 7-day-old Gushi chickens by adding exogenous corticosterone (CORT) to their diet and determined the microRNA (miRNA) expression profile of thymus tissues using RNA-seq technology. The results identified 51 differentially expressed miRNAs (DEMs), including 30 upregulated miRNAs and 21 downregulated miRNAs. Read More

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September 2021

TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response.

Nucleic Acids Res 2021 Sep 17. Epub 2021 Sep 17.

Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, USA.

Syngeneic mouse models are tumors derived from murine cancer cells engrafted on genetically identical mouse strains. They are widely used tools for studying tumor immunity and immunotherapy response in the context of a fully functional murine immune system. Large volumes of syngeneic mouse tumor expression profiles under different immunotherapy treatments have been generated, although a lack of systematic collection and analysis makes data reuse challenging. Read More

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September 2021

Insm1, Neurod1, and Pax6 promote murine pancreatic endocrine cell development through overlapping yet distinct RNA transcription and splicing programs.

G3 (Bethesda) 2021 Aug 26. Epub 2021 Aug 26.

Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.

Insm1, Neurod1, and Pax6 are essential for the formation and function of pancreatic endocrine cells. Here, we report comparative immunohistochemical, transcriptomic, functional enrichment, and RNA splicing analyses of these genes using gene knock-out mice. Quantitative immunohistochemical analysis confirmed that elimination of each of these three factors variably impairs the proliferation, survival, and differentiation of endocrine cells. Read More

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Interactome screening of C9orf72 dipeptide repeats reveals VCP sequestration and functional impairment by polyGA.

Brain 2021 Sep 17. Epub 2021 Sep 17.

Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.

Repeat expansions in the C9orf72 gene are a common cause of amyotrophic lateral sclerosis and frontotemporal lobar degeneration, two devastating neurodegenerative disorders. One of the proposed mechanisms of GGGGCC repeat expansion is their translation into non-canonical dipeptide repeats, which can then accumulate as aggregates and contribute to these pathologies. There are five different dipeptide repeat proteins (polyGA, polyGR, polyPR, polyPA and polyGP), some of which are known to be neurotoxic. Read More

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September 2021

Identification of BR biosynthesis genes in cotton reveals that GhCPD-3 restores BR biosynthesis and mediates plant growth and development.

Planta 2021 Sep 17;254(4):75. Epub 2021 Sep 17.

Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.

Main Conclusion: Brassinosteroid (BR) synthesis genes in different cotton species was comprehensively identified, and the participation of GhCPD-3 in the BR synthesis signaling pathway for regulating plant development was verified. Brassinosteroid is a natural steroidal phytohormone that plays fundamental roles in plant growth and development. In cotton, detailed characterization and functional validation of BR biosynthesis genes remain rare. Read More

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September 2021

and its outer protein Amuc_1100 regulates tryptophan metabolism in colitis.

Food Funct 2021 Sep 17. Epub 2021 Sep 17.

Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, P.R. China.

Dietary interventions, including dietary ingredients, nutrients and probiotics, exert anti-inflammatory effects in ulcerative colitis (UC). Our previous study showed that (), a promising probiotic, could protect against colitis the regulation of the immune response. However, whether it can restore aberrant tryptophan (Trp) metabolism during colitis remains unclear. Read More

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September 2021

Network pharmacology study on the mechanism of Qiangzhifang in the treatment of panic disorder.

Ann Transl Med 2021 Aug;9(16):1350

Department of Psychosomatic Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.

Background: Panic disorder (PD) is a kind of mental illness characterized by the symptom of recurring panic attacks. Qiangzhifang (QZF) is a novel decoction developed by Professor Zhaojun Yan based on a unique system of syndrome differentiation and clinical experience. It has achieved remarkable results after long-term clinical practice, but its mechanism of action is still unclear. Read More

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Identification of components of Caoguo using accelerated solvent extraction combined with gas chromatography-mass spectrometry integrated with network pharmacology on indigestion.

Ann Transl Med 2021 Aug;9(15):1247

Department of Pharmacy, The First Hospital of China Medical University, Shenyang, China.

Background: Caoguo (), a traditional Chinese medicine, is widely used as medicine and dietary spices. Volatile components are among its important bioactive constituents used to treatment of abdominal distension and pain, but the mechanism is not clear up to now. The purpose of this study was to develop a simple, sensitive, and accurate method to analyze and identify components of Caoguo and , and further investigate the therapeutic mechanism of Caoguo on indigestion using network pharmacology. Read More

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Diagnostic biomarkers and potential drug targets for coronary artery disease as revealed by systematic analysis of lncRNA characteristics.

Ann Transl Med 2021 Aug;9(15):1243

Department of Cardiology, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China.

Background: The expression profile of lncRNAs in coronary artery disease (CAD) patients has not yet been fully explored. Therefore, the current study aimed to investigate lncRNA-based prognostic biomarkers for CAD.

Methods: The expression profiles of lncRNA and messenger RNA (mRNA) were downloaded from the Gene Expression Omnibus (GEO) database. Read More

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Identification of an N6-methyladenosine (m6A)-related signature associated with clinical prognosis, immune response, and chemotherapy in primary glioblastomas.

Ann Transl Med 2021 Aug;9(15):1241

Department of Cerebrovascular Surgery, Engineering Technology Research Centre of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Zhujiang Hospital, Southern Medical University, Guangzhou, China.

Background: N6-methyladenosine (m6A) RNA methylation regulators play crucial role in tumorigenicity and progression. However, their biological significance in primary glioblastomas (GBM) has not been fully elucidated.

Methods: In the present study, we evaluated the 22 m6A RNA regulators using the integrated data of primary GBM samples from The Cancer Genome Atlas and Chinese Glioma Genome Atlas databases. Read More

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Identification of Immune-Related Subtypes and Characterization of Tumor Microenvironment Infiltration in Bladder Cancer.

Front Cell Dev Biol 2021 31;9:723817. Epub 2021 Aug 31.

State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China.

Tumors are closely related to the tumor microenvironment (TME). The complex interaction between tumor cells and the TME plays an indisputable role in tumor development. Tumor cells can affect the TME, promote tumor angiogenesis and induce immune tolerance by releasing cell signaling molecules. Read More

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A Co-Expression Network Reveals the Potential Regulatory Mechanism of lncRNAs in Relapsed Hepatocellular Carcinoma.

Front Oncol 2021 31;11:745166. Epub 2021 Aug 31.

Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China.

Background: The mechanistic basis for relapsed hepatocellular carcinoma (HCC) remains poorly understood. Recent research has highlighted the important roles of long non-coding RNAs (lncRNAs) in HCC. However, there are only a few studies on the association between lncRNAs and HCC relapse. Read More

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Identification of autophagy-related long non-coding RNA prognostic and immune signature for clear cell renal cell carcinoma.

Transl Androl Urol 2021 Aug;10(8):3317-3331

Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.

Background: Studies over the past decade have shown that long non-coding RNAs (lncRNAs) play an essential role in the tumorigenesis and progression of kidney renal clear cell carcinoma (KIRC). Meanwhile, autophagy has been demonstrated to regulate KIRC pathogenesis and targeting therapy resistance. However, the prognostic value of autophagy-related lncRNAs in KIRC patients has not been reported before. Read More

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Identification of novel biomarkers of prostate cancer through integrated analysis.

Transl Androl Urol 2021 Aug;10(8):3239-3254

Department of Urology Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Background: The current methods adopted to screen for prostate cancer (PCa) can sometimes be misleading and inaccurate. Moreover, for advanced stages of PCa, the current effect of treatment is not satisfactory for some patients. Accordingly, we aimed to identify new biomarkers for the diagnosis and prognosis of PCa. Read More

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Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation.

PeerJ 2021 27;9:e12091. Epub 2021 Aug 27.

Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China.

Stromal cell-derived factor-1 (SDF-1) and Exendin-4 (EX-4) play beneficial roles in promoting periodontal ligament stem cells (PDLSCs) osteogenic differentiation, while the detailed mechanism has not been clarified. In this study, we aimed to evaluate the biological mechanism of SDF-1 and EX-4 alone or synergistic application in regulating PDLSCs differentiation by RNA-sequencing (RNA-seq). A total of 110, 116 and 109 differentially expressed genes (DEGs) were generated in osteogenic medium induced PDLSCs treated by SDF-1, EX-4, and SDF-1+EX-4, respectively. Read More

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Increased expression predicts poor prognosis in hepatocellular carcinoma based on bioinformatics.

J Gastrointest Oncol 2021 Aug;12(4):1905-1926

Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, China.

Background: Liver cancer is one of the major causes of cancer death worldwide, incurring high mortality and a significant financial burden on the healthcare system. Abnormal RNA-binding proteins (RBPs) have been found to be associated with carcinogenesis in liver cancer. Among these, RNA-binding motif protein 12 () is located in the exon junction complex (EJC). Read More

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Underlying mechanism of sorafenib resistance in hepatocellular carcinoma: a bioinformatics study based on validated resistance-related genes.

J Gastrointest Oncol 2021 Aug;12(4):1895-1904

Department of Pharmacy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.

Background: Sorafenib, the first approved targeted therapy for advanced hepatocellular carcinoma (HCC), is often reported to comprised survival-benefit due to resistance. An underlying mechanism of resistance was proposed using bioinformatics analysis based on differentially expressed genes (DEGs) from microarrays. However, most DEGs were invalidated at both the expression level, and the role in causing resistance. Read More

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Risk characteristics with seven epithelial-mesenchymal transition-related genes are used to predict the prognosis of patients with hepatocellular carcinoma.

J Gastrointest Oncol 2021 Aug;12(4):1884-1894

Department of Oncology, Liyang People's Hospital, Liyang, China.

Background: Epithelial-mesenchymal transition (EMT)-related genes (ERGs) have been shown to play an important role in cancer invasion, tumor resistance, and tumor metastasis of hepatocellular carcinoma. This study sought to examine the prognostic value of ERGs and other pre-hepatoma genes.

Methods: Relevant data from The Cancer Genome Atlas (TCGA) were analyzed and synthesized. Read More

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FAT10 promotes hepatocellular carcinoma (HCC) carcinogenesis by mediating P53 degradation and acts as a prognostic indicator of HCC.

J Gastrointest Oncol 2021 Aug;12(4):1823-1837

The Second Department of Oncology, the Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China.

Background: With the advancement of hepatocellular carcinoma (HCC) treatment technology, the treatment options for HCC patients have increased. However, due to high heterogeneity, among other reasons, the five-year survival rate of patients is still very low. Currently, gene expression prognostic models can suggest more appropriate strategies for the treatment of HCC. Read More

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Bioinformatical identification of key genes regulated by IGF2BP2-mediated RNA N6-methyladenosine and prediction of prognosis in hepatocellular carcinoma.

Authors:
Qiang Wei

J Gastrointest Oncol 2021 Aug;12(4):1773-1785

Hepatological Surgery Department, Bethune International Peace Hospital of PLA, Shijiazhuang, China.

Background: The treatment of hepatocellular carcinoma (HCC), a malignant cancer with global spread, remains unsatisfactory, and novel prognostic biomarkers need to be identified. N6-methyladenosine (mA) has been found to regulate tumor initiation and progression through different mechanisms. As a dynamic and reversible messenger RNA (mRNA) modification, mA can be read by insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). Read More

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Identification of hub genes and functional modules in colon adenocarcinoma based on public databases by bioinformatics analysis.

J Gastrointest Oncol 2021 Aug;12(4):1613-1624

Department of Geratology Surgery, Xiangya Hospital, Central South University, Changsha, China.

Background: Colon adenocarcinoma (COAD) is one of the most common cancers in the world. Although an extensive effort has been made to elucidate its pathogenesis, the underlying molecular mechanisms and genetic characteristics remain elusive.

Methods: In this study, protein-coding transcript expression profiles of COAD were downloaded from the Cancer RNA-Seq Nexus (CRN) database. Read More

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The predictive value of RNA binding proteins in colon adenocarcinoma.

J Gastrointest Oncol 2021 Aug;12(4):1543-1557

Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, China.

Background: RNA binding proteins (RBPs) play an important role in regulating post-transcriptional gene expression and have been reported to be closely associated with the occurrence and development of tumors. However, the effect of RBPs in colon cancer remains unclear.

Methods: We downloaded clinical information and transcriptome data of colon adenocarcinoma (COAD) from The Cancer Genome Atlas database (TCGA) database. Read More

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Differential analysis of RNA methylation regulators in gastric cancer based on TCGA data set and construction of a prognostic model.

J Gastrointest Oncol 2021 Aug;12(4):1384-1397

Key Laboratory of Visceral Theory and Application in Traditional Chinese Medicine of Ministry of Education, Liaoning University of Traditional Chinese Medicine, Shenyang, China.

Background: Methylation is one of the common forms of RNA modification, which mainly include N6-methyladenosine (m6A), C5-methylcytidine (m5C), and N1-methyladenosine (m1A). Numerous studies have shown that RNA methylation is associated with tumor development. We aim to construct prognostic models of gastric cancer based on RNA methylation regulators. Read More

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Diagnostic and prognostic value of MATN3 expression in gastric carcinoma: TCGA database mining.

J Gastrointest Oncol 2021 Aug;12(4):1374-1383

Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.

Backgrounds: Globally, the high morbidity and mortality of gastric carcinoma (GC) have been one of the great challenges facing humanity. However, the early diagnosis of GC is still unknown. Matrilin-3 (MATN3) is a member of the extracellular matrix (ECM) protein family. Read More

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Characterization of functional sweetened condensed milk formulated with flavoring and sugar substitute.

Food Sci Nutr 2021 Sep 21;9(9):5119-5130. Epub 2021 Jul 21.

Department of Food Science and Technology Faculty of Biological Sciences North Tehran Branch Islamic Azad University Tehran Iran.

In the present study, the effect of sugar replacement and enrichment with cinnamon extract (CE) on the physicochemical, functional, and organoleptic properties of sweetened condensed milk (SCM) and the production of flavored functional dairy dessert was investigated. The results demonstrated that by adding CE (0.5 and 1%) and fructose sugar (50 and 100% replacement) in the formulation containing maltodextrin, the physicochemical, functional, and organoleptic properties of SCM samples were improved. Read More

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September 2021

Identifying the dynamic gene regulatory network during latent HIV-1 reactivation using high-dimensional ordinary differential equations.

Int J Comput Biol Drug Des 2018 28;11(1-2):135-153. Epub 2018 Mar 28.

Department of Biostatistics, The University of Texas School of Public Health, 1200 Pressler Street, Houston, TX, USA, 77030, USA.

Reactivation of latently infected cells has emerged as an important strategy for eradication of HIV. However, genetic mechanisms of regulation after reactivation remain unclear. We describe a five-step pipeline to study the dynamics of the gene regulatory network following a viral reactivation using high-dimensional ordinary differential equations. Read More

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Mechanism of Intervention in Cerebral Infarction: A Research Based on Chemoinformatics and Systematic Pharmacology.

Evid Based Complement Alternat Med 2021 6;2021:6789835. Epub 2021 Sep 6.

Hunan University of Chinese Medicine, Changsha, Hunan Province, China.

Objective: To explore the therapeutic targets, network modules, and coexpressed genes of intervention in cerebral infarction (CI), and to predict significant biological processes and pathways through network pharmacology. To explore the differential proteins of intervention in CI, conduct bioinformatics verification, and initially explain the possible therapeutic mechanism of intervention in CI through proteomics.

Methods: The TCM database was used to predict the potential compounds of Radix Rhei Et Rhizome, and the PharmMapper was used to predict its potential targets. Read More

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September 2021

TLR3 Serves as a Prognostic Biomarker and Associates with Immune Infiltration in the Renal Clear Cell Carcinoma Microenvironment.

J Oncol 2021 6;2021:3336770. Epub 2021 Sep 6.

Department of Urology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310006, China.

Background: Clear cell renal cancer (KIRC) is one of the most common cancers globally, with a poor prognosis. TLRs play a vital role in anticancer immunity and the regulation of the biological progress of tumour cells. However, the precise role of TLRs in KIRC is still ambiguous. Read More

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September 2021

Selection and Evaluation of a Thornless and HLB-Tolerant Bud-Sport of Pummelo Citrus With an Emphasis on Molecular Mechanisms.

Front Plant Sci 2021 31;12:739108. Epub 2021 Aug 31.

United States Department of Agriculture-Agriculture Research Service-United States Horticultural Research Laboratory, Fort Pierce, FL, United States.

The selection of elite bud-sports is an important breeding approach in horticulture. We discovered and evaluated a thornless pummelo bud-sport (TL) that grew more vigorously and was more tolerant to Huanglongbing (HLB) than the thorny wild type (W). To reveal the underlying molecular mechanisms, we carried out whole-genome sequencing of W, and transcriptome comparisons of W, TL, and partially recovered thorny "mutants" (T). Read More

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Identification of Biomarkers for Systemic Distribution of Nanovesicles From N6.2.

Front Immunol 2021 31;12:723433. Epub 2021 Aug 31.

Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States.

The ability of bacterial extracellular vesicles (EV) to transport biological molecules has increased the research to determine their potential as therapeutic agents. In this study, N6.2-derived nanovesicles (NV) were characterized to identify components that may serve as biomarkers in host-microbe interactions. Read More

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