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Ruth Ruiz Esparza-Garrido, Juan Manuel Rodríguez-Corona, Javier Enrique López-Aguilar, Marco Antonio Rodríguez-Florido, Ana Claudia Velázquez-Wong, Rubí Viedma-Rodríguez, Fabio Salamanca-Gómez, Miguel Ángel Velázquez-Flores
Expression changes for long non-coding RNAs (lncRNAs) have been identified in adult glioblastoma multiforme (GBM) and in a mixture of adult and pediatric astrocytoma. Since adult and pediatric astrocytomas are molecularly different, the mixture of both could mask specific features in each. We determined the global expression patterns of lncRNAs and messenger RNA (mRNAs) in pediatric astrocytoma of different histological grades. Transcript expression changes were determined with an HTA 2.0 array. lncRNA interactions with microRNAs and mRNAs were predicted by using an algorithm and the LncTar tool, respectively...
October 13, 2016: Molecular Neurobiology
Chenghua Du, Pan Pan, Yan Jiang, Qiuli Zhang, Jinsuo Bao, Chang Liu
BACKGROUND: Glioma is one of the most common primary malignancies in the brain or spine. The transcription factor (TF) CCAAT/enhancer binding protein beta (CEBPB) is important for maintaining the tumor initiating capacity and invasion ability. To investigate the regulation mechanism of CEBPB in glioma, microarray data GSE47352 was analyzed. METHODS: GSE47352 was downloaded from Gene Expression Omnibus, including three samples of SNB19 human glioma cells transduced with non-target control small hairpin RNA (shRNA) lentiviral vectors for 72 h (normal glioma cells) and three samples of SNB19 human glioma cells transduced with CEBPB shRNA lentiviral vectors for 72 h (CEBPB-silenced glioma cells)...
October 6, 2016: World Journal of Surgical Oncology
Heng Xia, Libin Zhang, Gang Wu, Chunhua Fu, Yan Long, Jun Xiang, Jianping Gan, Yanhong Zhou, Longjiang Yu, Maoteng Li
MiRNAs function in post-transcriptional regulation of gene expression and play very important roles in plant development. Lonicera japonica is one of the important medicinal plants in China. However, few studies on the discovery of conserved and novel miRNAs from L. japonica were reported. In this study, we employed deep sequencing technology to identify miRNAs in leaf and flower tissues of L. japonica. A total of 22.97 million clean reads from flower and leaf tissues were obtained, which generated 146 conserved miRNAs distributed in 20 families and 110 novel miRNAs...
2016: PloS One
Fan Yi, Xiao-Lei Tan, Xin Yan, Hai-Bo Liu
BACKGROUND: Lepidium meyenii Walpers (maca) is an herb known as a traditional nutritional supplement and widely used in Peru, North America, and Europe to enhance human fertility and treat osteoporosis. The secondary metabolites of maca, namely, maca alkaloids, macaenes, and macamides, are bioactive compounds, but their targets are undefined. METHODS: The pharmacophore-based PharmaDB targets database screening joint the ligand shape similarity-based WEGA validation approach is proposed to predict the targets of these unique constituents and was performed using Discovery Studio 4...
2016: Chinese Medicine
Junguo Wang, Fang Mei, Xia Gao, Shoulin Wang
Nasopharyngeal carcinoma (NPC) is the most common cancer originating from the nasopharynx, and can be induced by infection with Epstein-Barr virus (EBV). To study the mechanisms of EBV-associated NPC, a microarray of the GSE12452 dataset was analyzed. GSE12452 was downloaded from Gene Expression Omnibus and consisted of 31 NPC samples and 10 normal healthy nasopharyngeal tissue samples. The differentially-expressed genes (DEGs) were screened using the linear models for microarray data package in R. Using Database for Annotation, Visualization and Integrated Discovery software, potential functions of the DEGs were predicted by Gene Ontology and pathway enrichment analyses...
October 2016: Oncology Letters
Guo-Hua Jin, Wei Xu, Yang Shi, Li-Bo Wang
Gastric cancer (GC) is a prevalent cancer, which remains incurable, and therefore requires an alternative treatment method. Celecoxib is a nonsteroidal anti-inflammatory drug that targets cyclooxygenase-2, and exhibits anticancer effects. The present study aimed to investigate the anti-GC mechanism of celecoxib using bioinformatics methods. Gene expression datasets GSE56807 (GC tissues and normal gastric tissues) and GSE54657 (celecoxib-treated and non-treated human GC epithelial AGS cells) were downloaded from the Gene Expression Omnibus database...
October 2016: Oncology Letters
Bin Song, Juan Du, Ye Feng, Yong-Jian Gao, Ji-Sheng Zhao
The aim of the present study was to investigate the mechanisms of long non-coding RNAs (lncRNAs) in a gastric cancer cell line treated with celecoxib. The human gastric carcinoma cell line NCI-N87 was treated with 15 µM celecoxib for 72 h (celecoxib group) and an equal volume of dimethylsulfoxide (control group), respectively. Libraries were constructed by NEBNext Ultra RNA Library Prep kit for Illumina. Paired-end RNA sequencing reads were aligned to a human hg19 reference genome using TopHat2. Differentially expressed genes (DEGs) and lncRNAs were identified using Cuffdiff...
October 2016: Experimental and Therapeutic Medicine
Hongyan Li, Xiaonan Zhao, Jing Wang, Minru Zong, Hailing Yang
BACKGROUND: Sarcoidosis is a multisystemic inflammatory and granulomatous disease that occurs in almost all populations and affects multiple organs. Meanwhile, its most common manifestation is pulmonary sarcoidosis. This study aimed to identify effective biomarkers for the diagnosis and therapy of pulmonary sarcoidosis. METHODS: GSE16538 was downloaded from Gene Expression Omnibus, including 6 pulmonary sarcoidosis samples and 6 normal lung samples. Then, differentially expressed genes (DEGs) were identified by limma package in R...
September 25, 2016: Gene
Muhammad Shoaib, Adnan Ahmad Ansari, Sung-Min Ahn
MOTIVATION: In this era of biological big data, data integration has become a common task and a challenge for biologists. The Resource Description Framework (RDF) was developed to enable interoperability of heterogeneous datasets. The EBI-RDF platform enables an efficient data integration of six independent biological databases using RDF technologies and shared ontologies. However, to take advantage of this platform, biologists need to be familiar with RDF technologies and SPARQL query language...
September 25, 2016: Bioinformatics
Jiantao Zhang, Wenli Zhou, Ying Liu, Nan Li
Down syndrome (DS) is the most common birth defect in children. To investigate the mechanisms of DS, the present study analyzed the bisulfite‑sequencing (seq) data GSE42144, which was downloaded from the Gene Expression Omnibus. GSE42144 included DNA methylation data of three DS samples and three control samples, and RNA‑seq data of two DS samples and five control samples. The methylated sites in the bisulfite‑seq data were detected using Bismark and Bowtie2. The BiSeq tool was applied to determine differentially methylated regions and to identify adjacent genes...
September 26, 2016: Molecular Medicine Reports
Weiwei Fan, Shuang Chang, Xiumei Shan, Dejun Gao, Steven Qian Zhang, Jin Zhang, Nan Jiang, Duan Ma, Zuohua Mao
Toxoplasma rhoptry protein 16 (ROP16) is crucial in the host-pathogen interaction by acting as a virulent factor during invasion. To improve understanding of the molecular function underlying the effect of ROP16 on host cells, the present study analyzed the transcriptional profile of genes in the ROP16‑transfected SH‑SY5Y human neuroblastoma cell line. The transcriptional profile of the SH‑SY5Y human neuroblastoma cell line overexpressing ROP16 were determined by microarray analysis in order to determine the host neural cell response to the virulent factor...
September 21, 2016: Molecular Medicine Reports
Peizhan Chen, Xiaohua Duan, Mian Li, Chao Huang, Jingquan Li, Ruiai Chu, Hao Ying, Haiyun Song, Xudong Jia, Qian Ba, Hui Wang
Cadmium has been defined as type I carcinogen for humans, but the underlying mechanisms of its carcinogenic activity and its influence on protein-protein interactions in cells are not fully elucidated. The aim of the current study was to evaluate, systematically, the carcinogenic activity of cadmium with systems biology approaches. From a literature search of 209 studies that performed with cellular models, 208 proteins influenced by cadmium exposure were identified. All of these were assessed by Western blotting and were recognized as key nodes in network analyses...
November 1, 2016: Toxicology and Applied Pharmacology
Hamid Alavi Majd, Atefeh Talebi, Kambiz Gilany, Nasibeh Khayyer
BACKGROUND: Gene networks have generated a massive explosion in the development of high-throughput techniques for monitoring various aspects of gene activity. Networks offer a natural way to model interactions between genes, and extracting gene network information from high-throughput genomic data is an important and difficult task. OBJECTIVES: The purpose of this study is to construct a two-way gene network based on parametric and nonparametric correlation coefficients...
June 2016: Iranian Red Crescent Medical Journal
Zhikui Wang, Zhaoxia Wang, Zhongqi Zhou, Yueqin Ren
BACKGROUND: This study sought to investigate crucial genes correlated with diabetic nephropathy (DN), and their potential functions, which might contribute to a better understanding of DN pathogenesis. METHODS: The microarray dataset GSE1009 was downloaded from Gene Expression Omnibus, including 3 diabetic glomeruli samples and 3 healthy glomeruli samples. The differentially expressed genes (DEGs) were identified by LIMMA package. Their potential functions were then analyzed by the GO and KEGG pathway enrichment analyses using the DAVID database...
2016: BMC Nephrology
Xiang Jin, Xingang Liu, Xiaodan Li, Yinghui Guan
Introduction. Lung adenocarcinoma (LAC) is the most frequent type of lung cancer and has a high metastatic rate at an early stage. This study is aimed at identifying LAC-associated genes. Materials and Methods. GSE62950 downloaded from Gene Expression Omnibus included a DNA methylation dataset and an mRNA expression profiles dataset, both of which included 28 LAC tissue samples and 28 adjacent normal tissue samples. The differentially expressed genes (DEGs) were screened by Limma package in R, and their functions were predicted by enrichment analysis using TargetMine online tool...
2016: BioMed Research International
Changyu Zhou, Jiayu Li, Jiarui Li, Yingchun Wan, Tao Li, Piyong Ma, Yingjian Wang, Haiyan Sang
The aim of the present study was to identify the differentially expressed microRNAs (DEMs) between Lynch syndrome (LS) and the normal colonic (N-C) control samples, predict the target genes (TGs) and analyze the potential functions of the DEMs and TGs. The miRNA expression dataset GSE30454, which included data of 13 LS and 20 N-C tissue samples, was downloaded from the Gene Expression Omnibus. The classical t-test in Linear Models for Microarray Data package was used for DEM identification. TG prediction was performed using 5 databases...
September 2016: Oncology Letters
Liang-Yuan Chen, Zhao-Lei Cui, Fan-Cui Hua, Weng-Jing Yang, Ye Bai, Feng-Hua Lan
Dermatomyositis (DM) is a type of autoimmune inflammatory myopathy, which primarily affects the skin and muscle. The underlying mechanisms of DM remain poorly understood. The present study aimed to explore gene expression profile alterations, investigate the underlying mechanisms, and identify novel targets for DM. The GSE48280 dataset, which includes data from five DM and five normal muscle tissue samples, was obtained from the Gene Expression Omnibus. Firstly, differentially expressed genes (DEGs) were screened by limma package in R...
October 2016: Molecular Medicine Reports
Maryam Nazarieh, Andreas Wiese, Thorsten Will, Mohamed Hamed, Volkhard Helms
BACKGROUND: Identifying the gene regulatory networks governing the workings and identity of cells is one of the main challenges in understanding processes such as cellular differentiation, reprogramming or cancerogenesis. One particular challenge is to identify the main drivers and master regulatory genes that control such cell fate transitions. In this work, we reformulate this problem as the optimization problems of computing a Minimum Dominating Set and a Minimum Connected Dominating Set for directed graphs...
2016: BMC Systems Biology
Carolina Moretto Carnielli, Juliana Artier, Julio Cezar Franco de Oliveira, Maria Teresa Marques Novo-Mansur
Here we provide the mass-spectrometry and in silico interaction network dataset of proteins identified on our research article on surface proteomic analysis from Xanthomonas citri subsp. citri (XAC) cells grown in vivo (infectious) and in vitro (non-infectious, control) by 2D-DIGE approach. Fluorescence labeling of proteins were performed on intact cells followed by cellular lysis and labeled spots from 2D gel differing in abundance between the two conditions (ANOVA, p-value<0.05) were analyzed by a nano-electrospray tandem mass spectrometry Q-Tof Ultima API mass spectrometer (MicroMass/Waters) (LC-ESI-MS/MS)...
September 2016: Data in Brief
Jiajie Peng, Hongxiang Li, Yongzhuang Liu, Liran Juan, Qinghua Jiang, Yadong Wang, Jin Chen
BACKGROUND: The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs...
2016: BMC Genomics
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