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https://www.readbyqxmd.com/read/28075450/integrated-analysis-of-differentially-expressed-genes-and-pathways-in-triple%C3%A2-negative-breast-cancer
#1
Cancan Peng, Wenli Ma, Wei Xia, Wenling Zheng
Triple‑negative breast cancer (TNBC) is a heterogeneous disease characterized by an aggressive phenotype and reduced survival. The aim of the present study was to investigate the molecular mechanisms involved in the carcinogenesis of TNBC and to identify novel target molecules for therapy. The differentially expressed genes (DEGs) in TNBC and normal adjacent tissue were assessed by analyzing the GSE41970 microarray data using Qlucore Omics Explorer, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes...
January 4, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28075412/the-antagonistic-effect-of-mycotoxins-deoxynivalenol-and-zearalenone-on-metabolic-profiling-in-serum-and-liver-of-mice
#2
Jian Ji, Pei Zhu, Fangchao Cui, Fuwei Pi, Yinzhi Zhang, Yun Li, Jiasheng Wang, Xiulan Sun
Metabolic profiling in liver and serum of mice was studied for the combined toxic effects of deoxynivalenol (DON) and zearalenone (ZEN), through gas chromatography mass spectrum. The spectrum of serum and liver sample of mice, treated with individual 2 mg/kg DON, 20 mg/kg ZEN, and the combined DON + ZEN with final concentration 2 mg/kg DON and 20 mg/kg ZEN for 21 days, were deconvoluted, aligned and identified with MS DIAL. The data matrix was processed with univariate analysis and multivariate analysis for selection of metabolites with variable importance for the projection (VIP) > 1, t-test p value < 0...
January 10, 2017: Toxins
https://www.readbyqxmd.com/read/28058586/key-genes-in-stomach-adenocarcinoma-identified-via-network-analysis-of-rna-seq-data
#3
Li Shen, Lizhi Zhao, Jiquan Tang, Zhiwei Wang, Weisong Bai, Feng Zhang, Shouli Wang, Weihua Li
RNA-seq data of stomach adenocarcinoma (STAD) were analyzed to identify critical genes in STAD. Meanwhile, relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated. Gene expression data of STAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. Relationships with correlation coefficient > 0.6 were retained in the gene co-expression network. Functional enrichment analysis was performed for the genes in the network with DAVID and KOBASS 2...
January 5, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28031185/metadcn-meta-analysis-framework-for-differential-co-expression-network-detection-with-an-application-in-breast-cancer
#4
Li Zhu, Ying Ding, Cho-Yi Chen, Lin Wang, Zhiguang Huo, SungHwan Kim, Christos Sotiriou, Steffi Oesterreich, George C Tseng
MOTIVATION: Gene co-expression network analysis from transcriptomic studies can elucidate genegene interactions and regulatory mechanisms. Differential co-expression analysis helps further detect alterations of regulatory activities in case/control comparison. Co-expression networks estimated from single transcriptomic study is often unstable and not generalizable due to cohort bias and limited sample size. With the rapid accumulation of publicly available transcriptomic studies, co-expression analysis combining multiple transcriptomic studies can provide more accurate and robust results...
December 28, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28025995/prediction-of-key-genes-and-mirnas-responsible-for-loss-of-muscle-force-in-patients-during-an-acute-exacerbation-of-chronic-obstructive-pulmonary-disease
#5
Yanhong Duan, Min Zhou, Jian Xiao, Chaomin Wu, Lei Zhou, Feng Zhou, Chunling Du, Yuanlin Song
The present study aimed to identify genes and microRNAs (miRNAs or miRs) that were abnormally expressed in the vastus lateralis muscle of patients with acute exacerbations of chronic obstructive pulmonary disease (AECOPD). The gene expression profile of GSE10828 was downloaded from the Gene Expression Omnibus database, and this dataset was comprised of 4 samples from patients with AECOPD and 5 samples from patients with stable COPD. Differentially expressed genes (DEGs) were screened using the Limma package in R...
November 2016: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28003598/an-itraq-based-quantitative-proteomics-study-of-refractory-mycoplasma-pneumoniae-pneumonia-patients
#6
Jia-Lu Yu, Qi-Fang Song, Zhi-Wei Xie, Wen-Hui Jiang, Jia-Hui Chen, Hui-Feng Fan, Ya-Ping Xie, Gen Lu
Mycoplasma pneumoniae(MP) is a leading cause of community-acquired pneumonia in children and young adults. Although MP pneumonia is usually benign and self-limited, in some cases it can develop into a life-threating refractory MP pneumonia(RMPP). However, the pathogenesis of RMPP is poorly understood. The identification and characterization of proteins related to RMPP could provide "proof of principle" to facilitate appropriate diagnostic and therapeutic strategies for MP patients. In this study, we applied the quantitative proteomic technique(iTRAQ) to globally analyze MP-related proteins in serum samples from five RMPP and five non-refractory MP pneumonia(NRMPP) patients, and five healthy children...
December 22, 2016: Japanese Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28000890/combined-analysis-of-gene-expression-mirna-expression-and-dna-methylation-profiles-of-osteosarcoma
#7
Wenpeng Zhang, Shiliang Han, Kang Sun
Osteosarcoma (OS) is a common primary malignancy in children and adolescents with relative high survival rate after chemotherapy. While the toxicity of chemotherapy and personalized different response to chemotherapy makes it difficult for the selection of therapeutics and improvement of diagnosis. In this study, we conducted a combined analysis of three types of microarray datasets (gene expression, microRNA (miRNA) expression and DNA methylation) from the Gene Expression Omnibus (GEO). The differential expression genes (DEGs) and miRNAs (DEMI) were screened out via the limma package and differential methylation sites (DMS) were identified by the IMA package...
December 15, 2016: Oncology Reports
https://www.readbyqxmd.com/read/28000864/identification-of-therapeutic-targets-for-parkinson-s-disease-via-bioinformatics-analysis
#8
Na Dong, Xueqing Zhang, Qingjun Liu
The present study aimed to identify molecular targets that have important roles in the progression of Parkinson's disease. The gene expression profile dataset GSE7621 and the microRNA (miRNA) expression profile dataset GSE16658 were downloaded from the Gene Expression Omnibus database. R programing software was used to identify differentially expressed genes and miRNAs. Subsequently, enriched Gene Ontology terms of differentially expressed genes were obtained using the Database for Annotation, Visualization and Integrated Discovery...
December 14, 2016: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28000438/gogadget-an-r-package-for-interpretation-and-visualization-of-go-enrichment-results
#9
Benjamin Nota
Gene expression profiling followed by gene ontology (GO) term enrichment analysis can generate long lists of significant GO terms. To interpret these results and get biological insight in the data, filtering and rearranging these long lists of GO terms might be desirable. The R package gogadget provides functions to modify GO analysis results, with a simple filter strategy. Furthermore, it groups redundant GO terms with hierarchical clustering and presents the results in a colorful heatmap. The filtered GO term enrichment results can also be exported by the package for subsequent analysis in Cytoscape Enrichment Map...
December 21, 2016: Molecular Informatics
https://www.readbyqxmd.com/read/27987172/exploring-plant-co-expression-and-gene-gene-interactions-with-cornet-3-0
#10
Michiel Van Bel, Frederik Coppens
Selecting and filtering a reference expression and interaction dataset when studying specific pathways and regulatory interactions can be a very time-consuming and error-prone task. In order to reduce the duplicated efforts required to amass such datasets, we have created the CORNET (CORrelation NETworks) platform which allows for easy access to a wide variety of data types: coexpression data, protein-protein interactions, regulatory interactions, and functional annotations. The CORNET platform outputs its results in either text format or through the Cytoscape framework, which is automatically launched by the CORNET website...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27964719/pathway-collages-personalized-multi-pathway-diagrams
#11
Suzanne Paley, Paul E O'Maille, Daniel Weaver, Peter D Karp
BACKGROUND: Metabolic pathway diagrams are a classical way of visualizing a linked cascade of biochemical reactions. However, to understand some biochemical situations, viewing a single pathway is insufficient, whereas viewing the entire metabolic network results in information overload. How do we enable scientists to rapidly construct personalized multi-pathway diagrams that depict a desired collection of interacting pathways that emphasize particular pathway interactions? RESULTS: We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27959423/comparative-analysis-of-hepatocellular-carcinoma-and-cirrhosis-gene-expression-profiles
#12
Mingming Jiang, Qingfang Zeng, Suiping Dai, Huixia Liang, Fengying Dai, Xueling Xie, Kunlin Lu, Chunfang Gao
Gene expression data of hepatocellular carcinoma (HCC) was compared with that of cirrhosis (C) to identify critical genes in HCC. A total of five gene expression data sets were downloaded from Gene Expression Omnibus. HCC and healthy samples were combined as dataset HCC, whereas cirrhosis samples were included in dataset C. A network was constructed for dataset HCC with the package R for performing Weighted Gene Co‑expression Network Analysis. Modules were identified by cluster analysis with the packages flashClust and dynamicTreeCut...
January 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27956081/gene-markers-of-fracture-healing-in-early-stage-and-the-regulatory-mechanism-during-the-process-using-microarray-analysis
#13
Chengxue Wang, Baochang Qi, Lei Tan, Jieping Cheng
BACKGROUND: The aim of this study was to explore crucial markers and uncover the regulatory mechanisms of fracture healing in the early stage. METHODS: Gene expression profile of GSE45156 was downloaded, in which 3 fractured samples and 3 unfractured samples were used in our present study. Based on the threshold value, differentially expressed genes (DEGs) were selected between two kinds of samples using limma package in R. Enrichment analysis of these DEGs was performed by DAVID software...
December 9, 2016: Acta Orthopaedica et Traumatologica Turcica
https://www.readbyqxmd.com/read/27942860/comprehensive-gene-and-microrna-expression-profiling-reveals-a-role-for-mirnas-in-the-oncogenic-roles-of-sphk1-in-papillary-thyroid-cancer
#14
Weiwei Liang, Zhiwei Xie, Weiling Cui, Yan Guo, Lijuan Xu, Jueheng Wu, Hongyu Guan
PURPOSE: The oncogenic roles of sphingosine kinase 1 (SphK1) in various cancers, including thyroid cancer, have been well demonstrated. However, the microRNAs (miRNAs) associated with the oncogenic roles of SphK1 remain largely unknown. METHODS: Global gene and miRNA expression in TPC1-Vector and TPC1-SphK1 cells was analyzed using digital gene expression (DGE) analysis and small RNA-seq, respectively. miRNA-mRNA interactions were explored by microT-CDS, and the predicted networks were visualized using CytoScape(®)...
December 10, 2016: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/27924018/disgenet-a-comprehensive-platform-integrating-information-on-human-disease-associated-genes-and-variants
#15
Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I Furlong
The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. To provide the community with a resource free of these hurdles, we have developed DisGeNET (http://www.disgenet.org), one of the largest available collections of genes and variants involved in human diseases...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924014/the-string-database-in-2017-quality-controlled-protein-protein-association-networks-made-broadly-accessible
#16
Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork, Lars J Jensen, Christian von Mering
A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27922680/identification-of-key-genes-induced-by-platelet-rich-plasma-in-human-dermal-papilla-cells-using-bioinformatics-methods
#17
Haiyan Shen, Hanxiao Cheng, Haihua Chen, Jufang Zhang
Dermal papilla cells (DPCs) are located at the base of hair follicles, and are known to induce hair follicle regeneration. Platelet-rich plasma (PRP) functions in hair follicle regeneration. To investigate the influence of PRP on DPCs, the present study analyzed RNA‑seq data of human hair dermal papilla cells (HHDPCs) that were treated or untreated by PRP. The data included in the RNA‑seq were from two normal and two treated HHDPC samples. Following identification by Cuffdiff software, differentially expressed genes (DEGs) underwent enrichment analyses, and protein-protein interaction networks were constructed using Cytoscape software...
January 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27907142/ibisa_tools-a-computational-toolkit-for-ion-binding-state-analysis-in-molecular-dynamics-trajectories-of-ion-channels
#18
Kota Kasahara, Kengo Kinoshita
Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering...
2016: PloS One
https://www.readbyqxmd.com/read/27900679/bioinformatic-profiling-identifies-a-glucose-related-risk-signature-for-the-malignancy-of-glioma-and-the-survival-of-patients
#19
Shihong Zhao, Jinquan Cai, Jianlong Li, Guiqiu Bao, Di Li, Yongli Li, Xiuwei Zhai, Chuanlu Jiang, Lihua Fan
The aim of this study is to investigate the glucose metabolic status and its prognostic value in glioma. The Chinese Glioma Genome Atlas (CGGA), The Cancer Genome Atlas (TCGA), and GSE16011 datasets were used to develop the glucose-related signature. A cohort of 305 glioma samples with whole genome microarray expression data from the Chinese Glioma Genome Atlas database was included for discovery. TCGA and GSE16011 datasets were used for validation. Gene Set Enrichment Analysis (GSEA) and Cytoscape were used to explore the bioinformatic implication...
November 29, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27899966/analysis-of-the-molecular-mechanism-of-osteosarcoma-using-a-bioinformatics-approach
#20
Jianxun Yang, Ning Wang
The aim of this study was to explore the underlying molecular mechanism related to the process and progression of osteosarcoma (OS). The differentially expressed genes (DEGs) were downloaded from the Gene Expression Omnibus database. The pathway and gene ontology (GO) enrichment analysis, as well as transcription factor, tumor-associated gene and tumor suppressor gene analyses were performed to investigate the functions of DEGs. Next, the protein-protein interaction (PPI) network was constructed and module analysis was further assessed by cluster analysis with the overlapping neighborhood expansion (Cluster ONE) cytoscape plug-in...
November 2016: Oncology Letters
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