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https://www.readbyqxmd.com/read/28934958/integrated-network-analysis-to-explore-the-key-genes-regulated-by-parathyroid-hormone-receptor-1-in-osteosarcoma
#1
Donghui Guan, Honglai Tian
BACKGROUND: As an invasive malignant tumor, osteosarcoma (OS) has high mortality. Parathyroid hormone receptor 1 (PTHR1) contributes to maintaining proliferation and undifferentiated state of OS. This study is designed to reveal the action mechanisms of PTHR1 in OS. METHODS: Microarray dataset GSE46861, which included six PTHR1 knockdown OS samples and six control OS samples, was obtained from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were identified and then performed with enrichment analysis separately using the limma package and DAVID online tool...
September 21, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28927082/identification-of-target-gene-of-venous-thromboembolism-in-patients-with-lymphoma-via-microarray-analysis
#2
Pengfei Liu, Wenhua Jiang, Huilai Zhang
Patients with lymphoma are at high risk of developing venous thromboembolism (VTE). The purpose of the present study was to identify the target gene associated with VTE for patients with lymphoma. Microarray data was downloaded from the gene expression omnibus database (GSE17078), which comprised the control group, 27 normal blood outgrowth endothelial cell (BOEC) samples, and the case group, 3 BOEC samples of venous thrombosis with protein C deficiency. Differentially expressed genes (DEGs) were identified by the Limma package of R...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28924942/exploring-the-anti-proliferative-activity-of-pelargonium-sidoides-dc-with-in-silico-target-identification-and-network-pharmacology
#3
A S P Pereira, M J Bester, Z Apostolides
Pelargonium sidoides DC (Geraniaceae) is a medicinal plant indigenous to Southern Africa that has been widely evaluated for its use in the treatment of upper respiratory tract infections. In recent studies, the anti-proliferative potential of P. sidoides was shown, and several phenolic compounds were identified as the bioactive compounds. Little, however, is known regarding their anti-proliferative protein targets. In this study, the anti-proliferative mechanisms of P. sidoides through in silico target identification and network pharmacology methodologies were evaluated...
September 18, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/28914394/bioinformatics-based-identification-of-methylated-differentially-expressed-genes-and-related-pathways-in-gastric-cancer
#4
Hao Li, Jing-Wei Liu, Shuang Liu, Yuan Yuan, Li-Ping Sun
BACKGROUND AND AIMS: The aim of the study was to identify methylated-differentially expressed genes (MDEGs) in gastric cancer and investigate their potential pathways. METHODS: Expression profiling (GSE13911 and GSE29272) and methylation profiling (GSE25869 and GSE30601) data were obtained from GEO DataSets. Differentially expressed genes and differentially methylated genes were identified using GEO2R. Gene ontology and pathway enrichment analyses were performed for the MDEGs...
September 15, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28910750/analysis-of-methylation-profiling-data-of-hyperplasia-and-primary-and-metastatic-endometrial-cancers
#5
Xihai Wu, Jilan Miao, Jingyan Jiang, Fangmei Liu
OBJECTIVE: Endometrial cancer is a prevalent cancer, and its metastasis causes low survival rate. This study aims to utilize DNA methylation data to investigate the mechanism of the development and metastasis of endometrial cancer. STUDY DESIGN: Methylation profiling data were down-loaded from Gene Expression Omnibus, including 8 hyperplasias, 33 primary and 53 metastatic endometrial cancers. COHCAP package and annotation files were utilized to identify differentially methylated genes (DMGs) and CpG islands between the three different endometrial diseases...
September 1, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/28902399/using-the-contextual-hub-analysis-tool-chat-in-cytoscape-to-identify-contextually-relevant-network-hubs
#6
Tanja Muetze, David J Lynn
Highly connected nodes in biological networks are called network hubs. Hubs are topologically important to the structure of the network and have been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we provide a step-by-step protocol for using the Contextual Hub Analysis Tool (CHAT), an application within Cytoscape 3, which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene or protein expression data, and identify hub nodes that are more highly connected to contextual nodes than expected by chance...
September 13, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28902367/identification-of-hub-genes-key-mirnas-and-potential-molecular-mechanisms-of-colorectal-cancer
#7
Shasha Wu, Feixiang Wu, Zheng Jiang
Colorectal cancer (CRC) is the most common cancer of the digestive system. The aim of the present study was to identify the potential biomarkers and uncover the underlying mechanisms. The gene and miRNA expression profiles were obtained from GEO database. The differentially expressed genes (DEGs) and miRNAs (DE miRNAs) were identified by GEO2R. The gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed by KOBAS 3.0. The protein-protein interaction (PPI) network and miRNA-gene network were constructed by Cytoscape software...
August 29, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28901457/screening-and-identification-of-key-biomarkers-in-hepatocellular-carcinoma-evidence-from-bioinformatic-analysis
#8
Lin Li, Qingsong Lei, Shujun Zhang, Lingna Kong, Bo Qin
Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. Intense efforts have been made to elucidate the pathogeny, but the molecular mechanisms of HCC are still not well understood. To identify the candidate genes in the carcinogenesis and progression of HCC, microarray datasets GSE19665, GSE33006 and GSE41804 were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified, and function enrichment analyses were performed. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using STRING and Cytoscape...
September 7, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28901452/screening-critical-genes-associated-with-malignant-glioma-using-bioinformatics-analysis
#9
Yonggang Xu, Jie Wang, Yanbin Xu, Hong Xiao, Jianhua Li, Zhi Wang
Malignant gliomas are high‑grade gliomas, which are derived from glial cells in the spine or brain. To examine the mechanisms underlying malignant gliomas in the present study, the expression profile of GSE54004, which included 12 grade II astrocytomas, 33 grade III astrocytomas and 98 grade IV astrocytomas, was downloaded from the Gene Expression Omnibus. Using the Limma package in R, the differentially expressed genes (DEGs) in grade III, vs. grade II astrocytoma, grade IV, vs. grade II astrocytoma, and grade IV, vs...
September 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28901445/identification-of-genes-associated-with-castration%C3%A2-resistant-prostate-cancer-by-gene-expression-profile-analysis
#10
Chui Guo Huang, Feng Xi Li, Song Pan, Chang Bao Xu, Jun Qiang Dai, Xing Hua Zhao
Prostate cancer (CaP) is a serious and common genital tumor. Generally, men with metastatic CaP can easily develop castration‑resistant prostate cancer (CRPC). However, the pathogenesis and tumorigenic pathways of CRPC remain to be elucidated. The present study performed a comprehensive analysis on the gene expression profile of CRPC in order to determine the pathogenesis and tumorigenic of CRPC. The GSE33316 microarray, which consisted of 5 non‑castrated samples and 5 castrated samples, was downloaded from the gene expression omnibus database...
September 13, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28874807/integrated-analysis-of-copy-number-variations-and-gene-expression-profiling-in-hepatocellular-carcinoma
#11
Chenhao Zhou, Wentao Zhang, Wanyong Chen, Yirui Yin, Manar Atyah, Shuang Liu, Lei Guo, Yi Shi, Qinghai Ye, Qiongzhu Dong, Ning Ren
Hepatocellular carcinoma (HCC) is one of the top three cancer killers worldwide. To identify CNV-driven differentially expressed genes (DEGs) in HBV related HCC, this study integrated analysis of copy number variations (CNVs) and gene expression profiling. Significant genes in regions of CNVs were overlapped with those obtained from the expression profiling. 93 CNV-driven genes exhibiting increased expression in the duplicated regions and 45 showing decreased expression in the deleted regions were obtained, which duplications and deletions were mainly documented at chromosome 1 and 4...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28860812/an-integrated-analysis-for-long-noncoding-rnas-and-micrornas-with-the-mediated-competing-endogenous-rna-network-in-papillary-renal-cell-carcinoma
#12
Chuiguo Huang, Naijun Yuan, Liying Wu, Xiaofu Wang, Junqiang Dai, Pan Song, Fengxi Li, Changbao Xu, Xinghua Zhao
Papillary renal cell carcinoma (PRCC) is the second most common subtype of renal cell carcinoma, and it lacks effective therapeutic targets and prognostic molecular biomarkers. Attention has been increasingly focused on long noncoding RNAs (lncRNAs), which can act as competing endogenous RNA (ceRNA) to compete for shared microRNAs (miRNAs) in the tumorigenesis of human tumors. Therefore, to clarify the functional roles of lncRNAs with respect to the mediated ceRNA network in PRCC, we comprehensively integrated expression profiles, including data on mRNAs, lncRNAs and miRNAs obtained from 289 PRCC tissues and 32 normal tissues in The Cancer Genome Atlas...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28858211/cytocluster-a-cytoscape-plugin-for-cluster-analysis-and-visualization-of-biological-networks
#13
Min Li, Dongyan Li, Yu Tang, Fangxiang Wu, Jianxin Wang
Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function...
August 31, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28836827/analyzing-the-lncrna-mirna-and-mrna-regulatory-network-in-prostate-cancer-with-bioinformatics-software
#14
Jin-Hua He, Ze-Ping Han, Mao-Xian Zou, Li Wang, Yu Bing Lv, Jia Bin Zhou, Ming-Rong Cao, Yu-Guang Li
Information processing tools and bioinformatics software have significantly advanced researchers' ability to process and analyze biological data. Molecular data from human and model organism genomes help researchers identify topics for study, which, in turn, improves predictive accuracy, facilitates the identification of relevant genes, and simplifies the validation of laboratory data. The objective of this study was to explore the regulatory network constituted by long noncoding RNA (lncRNA), miRNA, and mRNA in prostate cancer (PCa)...
August 24, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28834917/microrna-expression-profiling-and-bioinformatics-analysis-of-dysregulated-micrornas-in-obstructive-sleep-apnea-patients
#15
Kun Li, Peng Wei, Yanwen Qin, Yongxiang Wei
Obstructive sleep apnea (OSA) is a common chronic obstructive sleep disease in clinic. The purpose of our study was to use bioinformatics analysis to identify microRNAs (miRNAs) that are differentially expressed between OSA patients and healthy controls.Serum samples were collected from OSA patients and healthy controls. To better reveal the sample specificity of differentially expressed microRNAs, supervised hierarchical clustering was conducted. We used the microT-CDS and TargetScan databases to predict target genes of the differentially expressed microRNAs and selected the common genes...
August 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28834871/bioinformatics-analysis-of-gene-expression-profiling-for-identification-of-potential-key-genes-among-ischemic-stroke
#16
Kaihua Zhai, Xiangli Kong, Boyu Liu, Jiyu Lou
This study aimed to identify the key differentially expressed genes (DEGs) following ischemic stroke (IS).The GSE22255 microarray dataset, which contains samples from peripheral blood mononuclear cells of 20 IS patients and 20 sex- and age-matched controls, was downloaded from the Gene Expression Omnibus. After data pre-processing, DEGs were identified using the Linear Models for Microarray Data package in R. The Search Tool for the Retrieval of Interacting Genes database was used to predict the interactions among the products of DEGs, and then Cytoscape software was used to visualize the protein-protein interaction (PPI) network...
August 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28819918/network-analysis-of-se-and-zn-related-proteins-in-the-serum-proteomics-expression-profile-of-the-endemic-dilated-cardiomyopathy-keshan-disease
#17
Sen Wang, Yanyan Lv, Yingting Wang, Peiru Du, Wuhong Tan, Mikko J Lammi, Xiong Guo
Keshan disease (KD) is an endemic cardiomyopathy with high mortality. Selenium (Se) and zinc (Zn) deficiencies are closely related to KD. The molecular mechanism of KD pathogenesis is still unclear. There are only few studies on the interaction of trace elements and proteins associated with the pathogenesis of KD. In this study, isobaric tags for relative and absolute quantitation (iTRAQ)-coupled two-dimensional liquid chromatography tandem mass spectrometry (2DLC-MS/MS) technique analysis was used to analyze the differential expression of proteins from serum samples...
August 18, 2017: Biological Trace Element Research
https://www.readbyqxmd.com/read/28810559/identification-of-key-genes-and-pathways-associated-with-obesity-in-children
#18
Ling Li, Guangyu Wang, Ning Li, Haiyan Yu, Jianping Si, Jiwen Wang
The present study aimed to identify potential key genes and pathways in obese children in order to explore possible molecular mechanisms associated with child obesity. The array dataset GSE29718 was downloaded from the Gene Expression Omnibus database. Subcutaneous adipose tissue samples derived from 7 obese children and 8 lean children were selected for the analysis. Differentially expressed genes (DEGs) in samples from obese children compared with those from lean children were analyzed by the limma package...
August 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28800317/identification-of-prostate-cancer-hub-genes-and-therapeutic-agents-using-bioinformatics-approach
#19
Enhao Fang, Xiuqing Zhang, Qi Wang, Daoming Wang
BACKGROUND: Prostate cancer (PCa) is the most common and the second leading cause of cancer-related death among men in America. As the molecular mechanism of PCa has not yet been completely discovered, identification of hub genes and potential drug of this disease is an important area of research that could provide new insights into exploring the mechanisms underlying PCa. OBJECTIVE: The aim of this study was to identify potential biomarkers and novel drug for prostate cancer treatment...
July 30, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28799567/identification-of-breast-cancer-mechanism-based-on-weighted-gene-coexpression-network-analysis
#20
X Guo, H Xiao, S Guo, L Dong, J Chen
Our gene expression-profiling analysis aimed to explain the mechanism of breast cancer development by identifying key pathways and constructing networks of related transcription factors (TFs) and microRNAs (miRNAs) in breast cancer tissues. Gene expression profiles of normal and breast cancer tissues were downloaded to identify differentially expressed genes (DEGs). Coexpression modules were explored using weighted gene coexpression network analysis (WGCNA). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to discover the enriched functionally associated gene groups and define pathways in breast cancer, respectively...
August 2017: Cancer Gene Therapy
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