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Hongfang Li, Yuzhi Zhen, Yunshuang Geng, Junyan Feng, Jun Wang, Hongsong Zhang
BACKGROUND The aim of this study was to identify some key genes related to the pathogenesis of thoracic aortic aneurysm (TAA) and gain more insights to the molecular mechanism of TAA. MATERIAL AND METHODS The expression profile of GSE9106 was downloaded from the Gene Expression Omnibus (GEO) database. The data contained 58 TAA peripheral blood samples and 36 normal peripheral blood samples. The differently expressed genes (DEGs) between the TAA samples and the normal samples were identified via limma package of R...
March 14, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
F Wu, S Wu, X Gou
Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cancer in adults. The aim of this study is to identify the biomarkers and potential molecular mechanisms of ccRCC. Three gene expression profiles and two miRNA expression profiles were downloaded from GEO database. A total of 330 up-regulated differentially expressed genes (DEGs), 545 down-regulated DEGs, 26 up-regulated differentially expressed miRNAs (DEMs) and 11 down-regulated DEMs were identified by GEO2R. The gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed by KOBAS software...
2018: Neoplasma
Fucai Tang, Zhaohui He, Hanqi Lei, Yuehan Chen, Zechao Lu, Guohua Zeng, Hangtao Wang
The purpose of the present study was to identify key genes and investigate the related molecular mechanisms of bladder cancer (BC) progression. From the Gene Expression Omnibus database, the gene expression dataset GSE7476 was downloaded, which contained 43 BC samples and 12 normal bladder tissues. GSE7476 was analyzed to screen the differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for the DEGs using the DAVID database, and a protein‑protein interaction (PPI) network was then constructed using Cytoscape software...
March 9, 2018: Molecular Medicine Reports
Hailing Yang, Xiaofei Zhang, Guangda Xin
BACKGROUND: Recent studies have reported that mesenchymal stem cells (MSCs) exert therapeutic effects on the treatment of diabetic nephropathy (DN), but the underlying mechanisms remain unclear. METHODS: A dataset GSE65561 was obtained from Gene Expression Omnibus (GEO) database, which contained four healthy control samples (group 1), four healthy controls samples co-cultured with MSCs (group 2), five DN samples (group 3) and five DN samples co-cultured with MSCs (group 4)...
March 13, 2018: Renal Failure
Yanxiong Gan, Shichao Zheng, Jiaqi Zhao, Chen Zhang, Tianhui Gao, Wan Liao, Qiang Fu, Chaomei Fu
ETHNOPHARMACOLOGICAL RELEVANCE: Curcuma phaeocaulis Val. (CP), as the vital medicines for blood-breaking and disorder-eliminating, has been widely used for hepatitis with good curative effects. Owing to the complexity of traditional Chinese medicine, the pharmacological mechanism of CP remains unclear. To solve this problem, a protein network module-based approach was proposed in this study. MATERIALS AND METHODS: Firstly, the content of active components of CP was detected based on HPLC-DAD...
March 8, 2018: Journal of Ethnopharmacology
Orlando Contreras-López, Tomás C Moyano, Daniela C Soto, Rodrigo A Gutiérrez
The rapid increase in the availability of transcriptomics data generated by RNA sequencing represents both a challenge and an opportunity for biologists without bioinformatics training. The challenge is handling, integrating, and interpreting these data sets. The opportunity is to use this information to generate testable hypothesis to understand molecular mechanisms controlling gene expression and biological processes (Fig. 1). A successful strategy to generate tractable hypotheses from transcriptomics data has been to build undirected network graphs based on patterns of gene co-expression...
2018: Methods in Molecular Biology
Yin Li, Fengxia Zhang, Yan Cong, Yun Zhao
Sepsis is a type of systemic inflammatory response syndrome caused by infection. The present study aimed to examine key genes and microRNAs (miRNAs) involved in the pathogenesis of sepsis. The GSE13205 microarray dataset, downloaded from the Gene Expression Omnibus was analyzed using bioinformatics tools, and included muscle biopsy specimens of 13 patients with sepsis and eight healthy controls. The differentially expressed genes (DEGs) in samples from patients with sepsis were identified using the Linear Models for Microarray package in R language...
March 1, 2018: Molecular Medicine Reports
Yang Ding, Pengfei Liu, Shengsheng Zhang, Lin Tao, Jianmin Han
Oral squamous cell carcinoma (OSCC) is one of the most common malignancies and its survival rate has barely improved over the past few decades. The purpose of this study was to screen pathogenic genes of OSCC via microarray analysis. The mRNA expression microarray datasets (GSE2280 and GSE3524) were downloaded from the Gene Expression Omnibus (GEO) database. In GSE2280, there were 22 OSCC samples without metastasis and 5 OSCC samples with lymph node metastasis. In GSE3524, there were 16 OSCC samples and 4 normal tissue samples...
February 27, 2018: International Journal of Molecular Medicine
Saeideh Jalali, Amir Zarrinhaghighi, Saman Sadraei, Younes Ghasemi, Amirhossein Sakhteman, Pouya Faridi
Background The plant Nardostachys jatamansi from Valerianaceae family is a well known antidepressant plant and has historically been used in traditional medicine. As N. jatamansi contains many different compounds, to identify its mechanisms of action, we need a network-based study. Network-based studies are becoming an increasingly important tool in understanding the mechanisms of actions of drugs. Systems pharmacology (SP) and bioinformatics are two emerging tools that use computation to develop an understanding of drug actions in molecular and cellular levels...
March 5, 2018: Current Drug Metabolism
Yuting Liang, Longwei Qiao, Xia Peng, Zelin Cui, Yue Yin, Huanjin Liao, Min Jiang, Li Li
Mast cells are important effector cells of the immune system, and mast cell-derived exosomes carrying RNAs play a role in immune regulation. However, the molecular function of mast cell-derived exosomes is currently unknown, and here, we identify differentially expressed genes (DEGs) in mast cells and exosomes. We isolated mast cells derived exosomes through differential centrifugation and screened the DEGs from mast cell-derived exosomes, using the GSE25330 array dataset downloaded from the Gene Expression Omnibus database...
2018: American Journal of Translational Research
Lei-Lei Zhou, Xiao-Yue Xu, Jie Ni, Xia Zhao, Jian-Wei Zhou, Ji-Feng Feng
OBJECTIVES: Due to the low incidence and the heterogeneity of subtypes, the biological process of T-cell lymphomas is largely unknown. Although many genes have been detected in T-cell lymphomas, the role of these genes in biological process of T-cell lymphomas was not further analyzed. METHODS: Two qualified datasets were downloaded from Gene Expression Omnibus database. The biological functions of differentially expressed genes were evaluated by gene ontology enrichment and KEGG pathway analysis...
March 5, 2018: European Journal of Haematology
Jing Wang, Chun-Lin Li, Lu-Lu Bai, Qiang-Hu Tang, Rui-Yuan Zhang, Ting-Li Han, Yu-Ming Guo, Philip N Baker, Yin-Yin Xia, Bai-Jie Tu
OBJECTIVE: To analyze the changes in endogenous small molecule metabolites after benzo[a]pyrene (B[a]P) exposure in rat cerebral cortex and explore the mechanism of B[a]P neurotoxicity. METHODS: Five-day-old SD rats were subjected to gavage administration of 2 mg/kg B[a]P for 7 consecutive weeks. After the exposure, the rats were assessed for spatial learning ability using Morris water maze test, ultrastructural changes of the cortical neurons under electron microscope, and metabolite profiles of the cortex using GC/MS...
February 20, 2018: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
Anne F Voor In 't Holt, Juliëtte A Severin, Margot B H Hagenaars, Inge de Goeij, Diederik Gommers, Margreet C Vos
Background: Emergence of multidrug-resistant Pseudomonas aeruginosa is of global concern. We aimed to identify epidemiological relationships, the most common way of transmission, and risk factors for presence of Verona Integron-encoded Metallo-β-lactamase (VIM)-positive P. aeruginosa (VIM-PA). Methods: We conducted a network analysis and matched case-control studies (1:2:2). Controls were hospital-based and matched with cases for ward, day of admission (control group 1 and 2) and time between admission and the identification of VIM-PA (control group 1)...
2018: Antimicrobial Resistance and Infection Control
Jian Ji, Pei Zhu, Ivana Blaženović, Fangchao Cui, Morteza Gholami, Jiadi Sun, Jean Habimana, Yinzhi Zhang, Xiulan Sun
Urine metabolic profiling of mice was conducted utilizing gas chromatography-mass spectrometry (GC-MS) to investigate the combinatory effect of mycotoxins deoxynivalenol (DON) and zearalenone (ZEN) on the metabolism of the mice. Experiments were conducted by means of five-week-old mice which were individually exposed to 2 mg/kg DON, 20 mg/kg ZEN and the mixture of DON and ZEN (2 mg/kg and 20 mg/kg, respectively). The intragastric administration was applied for three weeks and urine samples were collected for metabolic analysis...
February 28, 2018: Scientific Reports
Egle Strainiene, Mindaugas Binkis, Silvija Urnikyte, Vaidotas Stankevicius, Ausra Sasnauskiene, Gabrielis Kundrotas, Andrius Kazlauskas, Kestutis Suziedelis
BACKGROUND: Since the first evidence suggesting existence of stem-like cancer cells, the process of cells reprogramming to the stem cell state remains as an attractive tool for cancer stemness research. Current knowledge in the field of cancer stemness, indicates that the microenvironment is a fundamental regulator of cell behavior. With regard to this, we investigated the changes of genome wide gene expression in reprogrammed human colon normal epithelial CRL-1831 and colon carcinoma DLD1 cell lines grown under more physiologically relevant three-dimensional (3D) cell culture microenvironment compared to 2D monolayer...
February 27, 2018: BMC Cancer
Chunguang Li, Liangtao Luo, Sheng Wei, Xiongbiao Wang
Invasive ductal carcinoma (IDC) is a common histological type of breast cancer. The aim of this study was to identify the potential crucial genes associated with IDC and to provide valid biological information for further investigations. The gene expression profiles of GSE10780 which contained 42 histologically normal breast tissues and 143 IDC tissues were downloaded from the GEO database. Functional and pathway enrichment analysis of differentially expressed genes (DEGs) were performed and protein-protein interaction (PPI) network was analyzed using Cytoscape...
January 23, 2018: Oncotarget
Yong Ni, Chengrui Jiang
This study aimed to identify the potential target genes for the treatment of ankylosing spondylitis (AS).Dataset GSE25101 was downloaded from Gene Expression Omnibus, including 16 AS and 16 normal control blood samples. Differentially expressed genes (DEGs) were identified using unmatched t-test in limma package with adjusted P < .05. Gene ontology-biological process (GO-BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted using multifaceted analysis tool for human transcriptome...
February 2018: Medicine (Baltimore)
Xue-Qing Hu, Bin Wei, Ya-Nan Song, Qing Ji, Qi Li, Yun-Quan Luo, Wen-Hai Wang, Shi-Bing Su
OBJECTIVES: This study aims to investigate the metabolic profiles of postoperative colorectal cancer (PCRC) patients with different traditional Chinese medicine (TCM) syndromes and to discuss the metabolic mechanism under PCRC progression and TCM syndrome classification. METHODS: Fifty healthy controls (HC) and 70 PCRC patients, including 10 Dampness and heat syndrome (DHS), 33 Spleen deficiency syndrome (SDS), 19 Liver and kidney Yin deficiency syndrome (LKYDS) and 8 with non-TCM syndrome (NS) were enrolled...
February 2018: Complementary Therapies in Medicine
Rita Ferreira, Fábio Trindade, Rui Vitorino
Proteomics is a technology that allows to decipher the molecular networks involved in the regulation of biological processes such as spermatogenesis. Sertoli cells (SCs) are key players in the paracrine control of this process. Envisioning to increase the knowledge on the molecular networks harbored in SCs, we propose a methodology based on GeLC-MS/MS for the characterization of these cells' proteome. Proteins are separated by SDS-PAGE hyphenated to HPLC and identified by mass spectrometry. The integration of data with bioinformatics tools such as ClueGO + CluePedia from Cytoscape allows the identification of the biological pathways more prevalent in SCs, and that might be modulated by pathophysiological conditions...
2018: Methods in Molecular Biology
Wufeng Fan, Guangming Ye
In order to identify the potential pathogenesis of hepatocellular carcinoma (HCC) developing from cirrhosis, a microarray‑based transcriptome profile was analyzed. The GSE63898 expression profile was downloaded from the Gene Expression Omnibus database, which included data from 228 HCC tissue samples and 168 cirrhotic tissue samples. The Robust Multi‑array Average in the Affy package of R was used for raw data processing and Student's t‑test was used to screen differentially expressed genes (DEGs). An enrichment analysis was then conducted using the Database for Annotation, Visualization and Integrated Discovery online tool, and the protein‑protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes and Cytoscape...
February 2, 2018: Molecular Medicine Reports
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