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Microarray gene expression meta-analysis

Eugenia Sanchez, Eliane Küpfer, Daniel J Goedbloed, Arne W Nolte, Tim Lüddecke, Stefan Schulz, Miguel Vences, Sebastian Steinfartz
The postembryonic development of amphibians has been characterized as divided into three predominant periods, hereafter named primary developmental stages: premetamorphosis (PreM), prometamorphosis (ProM), metamorphic climax (Meta), and completion of metamorphosis (PostM), largely based on examination of anuran development. Here, we categorized the postembryonic development of larvae of a poisonous fire salamander (Salamandra salamandra) by integrating morphology and gene expression (transcriptomic) data. Morphological analysis revealed three distinct clusters suggestive of PreM, ProM, and Meta, which were confirmed in parallel by microarray-derived gene expression analysis...
March 5, 2018: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
Amit Katiyar, Sujata Sharma, Tej P Singh, Punit Kaur
Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune diseases predominantly multiple sclerosis (MS). Though EMS and MS are evidently diverse in their phenotype, they are linked by a common autoimmune condition or immunodeficiency which could play a role in the expansion of endometriosis and possibly increase the risk of developing MS in women with EMS. However, the common molecular links connecting EMS with MS are still unclear. We conducted a meta-analysis of microarray experiments focused on EMS and MS with their respective controls...
2018: Frontiers in Genetics
Junghyun Jung, Go Woon Kim, Woosuk Lee, Changsoo Mok, Sung Hyun Chung, Wonhee Jang
Ample evidence indicates that insulin resistance (IR) is closely related to white adipose tissue (WAT), but the underlying mechanisms of IR pathogenesis are still unclear. Using 352 microarray datasets from seven independent studies, we identified a meta-signature which comprised of 1,413 genes. Our meta-signature was also enriched in overall WAT in in vitro and in vivo IR models. Only 12 core enrichment genes were consistently enriched across all IR models. Among the meta-signature, we identified a drug signature made up of 211 genes with expression levels that were co-regulated by thiazolidinediones and metformin using cross-species analysis...
February 27, 2018: Scientific Reports
Somayeh Sharifi, Abbas Pakdel, Mansour Ebrahimi, James M Reecy, Samaneh Fazeli Farsani, Esmaeil Ebrahimie
Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the main agents that cause severe mastitis disease with clinical signs in dairy cattle. Rapid detection of this disease is so important in order to prevent transmission to other cows and helps to reduce inappropriate use of antibiotics. With the rapid progress in high-throughput technologies, and accumulation of various kinds of '-omics' data in public repositories, there is an opportunity to retrieve, integrate, and reanalyze these resources to improve the diagnosis and treatment of different diseases and to provide mechanistic insights into host resistance in an efficient way...
2018: PloS One
Wei Zhong, Lianzhi Dai, Jing Liu, Song Zhou
Cholangiocarcinoma (CCA) is characterized by delayed diagnosis and poor survival rate. Research efforts have focused on novel diagnostic technologies for this type of cancer. Transcriptomic microarray technology is a useful research strategy for investigating the molecular properties of CCA. The objective of the present study was to identify candidate biomarkers with high potential for clinical application in CCA using a meta‑analysis‑based approach. Gene expression profiles of CCA were downloaded from the Gene Expression Omnibus database for integrated analysis...
February 12, 2018: Molecular Medicine Reports
Richa K Makhijani, Shital A Raut, Hemant J Purohit
Cancer is one of the leading causes of mortality worldwide, and in particular, breast cancer in women, prostate cancer in men, and lung cancer in both women and men. The present study aimed to identify a common set of genes which may serve as indicators of important molecular and cellular processes in breast, prostate and lung cancer. Six microarray gene expression profile datasets [GSE45827, GSE48984, GSE19804, GSE10072, GSE55945 and GSE26910 (two datasets for each cancer)] and one RNA-Seq expression dataset (GSE62944 including all three cancer types), were downloaded from the Gene Expression Omnibus database...
February 2018: Oncology Letters
Hiroshi Nishiwaki, Mikako Ito, Shuto Negishi, Sayaka Sobue, Masatoshi Ichihara, Kinji Ohno
BACKGROUND: Molecular hydrogen exerts its effect on multiple pathologies, including oxidative stress, inflammation, and apoptosis. However, its molecular mechanisms have not been fully elucidated. In order to explore the effects of molecular hydrogen, we meta-analyzed gene expression profiles modulated by molecular hydrogen. METHODS: We performed microarray analysis of the mouse liver with or without drinking hydrogen water. We also integrated two previously reported microarray datasets of the rat liver into meta-analyses...
February 9, 2018: Free Radical Research
Yue-Ya Liang, Jia-Cheng Huang, Rui-Xue Tang, Wen-Jie Chen, Peng Chen, Wei-Luan Cen, Ke Shi, Li Gao, Xiang Gao, An-Gui Liu, Xiao-Tong Peng, Gang Chen, Su-Ning Huang, Ye-Ying Fang, Yong-Yao Gu
BACKGROUND: To examine the clinical value of miR-198-5p in lung squamous cell carcinoma (LUSC). METHODS: Gene Expression Omnibus (GEO) microarray datasets were used to explore the miR-198-5p expression and its diagnostic value in LUSC. Real-time reverse transcription quantitative polymerase chain reaction was used to evaluate the expression of miR-198-5p in 23 formalin-fixed, paraffin-embedded (FFPE) LUSC tissues and corresponding non-cancerous tissues. The correlation between miR-198-5p expression and clinic pathological features was assessed...
February 2, 2018: World Journal of Surgical Oncology
Jie-Yu Wang, Jia-Cheng Huang, Gang Chen, Dan-Ming Wei
For the purpose of demonstrating the clinical value and unraveling the molecular mechanisms of micro RNA (miR)-1-3p in colorectal carcinoma (CRC), the present study collected expression and diagnostic data from Gene Expression Omnibus (GEO), ArrayExpress and existing literature to conduct meta‑analyses and diagnostic tests. Furthermore, the potential targets of miR‑1‑3p were attained from datasets that transfected miR‑1‑3p into CRC cells, online prediction databases and differentially expressed genes from The Cancer Genome Atlas and literature...
February 1, 2018: Molecular Medicine Reports
Shang-Pen Huang, Yu-Chan Chang, Qie Hua Low, Alexander T H Wu, Chi-Long Chen, Yuan-Feng Lin, Michael Hsiao
There is variation in the survival and therapeutic outcome of patients with glioblastomas (GBMs). Therapy resistance is an important challenge in the treatment of GBM patients. The aim of this study was to identify Temozolomide (TMZ) related genes and confirm their clinical relevance. The TMZ-related genes were discovered by analysis of the gene-expression profiling in our cell-based microarray. Their clinical relevance was verified by in silico meta-analysis of the Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) datasets...
December 26, 2017: Oncotarget
Xiaona He, Cheng Zhang, Chao Shi, Quqin Lu
Compared to other types of lung cancer, lung adenocarcinoma patients with a history of smoking have a poor prognosis during the treatment of lung cancer. How lung adenocarcinoma-related genes are differentially expressed between smoker and non-smoker patients has yet to be fully elucidated. We performed a meta-analysis of four publicly available microarray datasets related to lung adenocarcinoma tissue in patients with a history of smoking using R statistical software. The top 50 differentially expressed genes (DEGs) in smoking vs...
January 8, 2018: Oncology Reports
Rui Wang, Yuxing Cai, Baoping Zhang, Zhengxia Wu
The present study aimed to perform screening of a gene signature for the discrimination and prognostic prediction of stage I and II lung squamous carcinoma. A microarray meta‑analysis was performed to identify differentially expressed genes (DEGs) between stage I and II lung squamous carcinoma samples in seven microarray datasets collected from the Gene Expression Omnibus database via the MetaQC and MetaDE package in R. The important DEGs were selected according to the betweenness centrality value of the protein‑protein interaction (PPI) network...
December 19, 2017: International Journal of Molecular Medicine
Hai-Biao Yan, Jia-Cheng Huang, You-Rong Chen, Jian-Ni Yao, Wei-Ning Cen, Jia-Yi Li, Yi-Fan Jiang, Gang Chen, Sheng-Hua Li
PURPOSE: To investigate the clinical value and potential molecular mechanisms of miR-1 in clear cell renal cell carcinoma (ccRCC). METHODS: We searched the Gene Expression Omnibus (GEO), ArrayExpress, several online publication databases and the Cancer Genome Atlas (TCGA). Continuous variable meta-analysis and diagnostic meta-analysis were conducted, both in Stata 14, to show the expression of miR-1 in ccRCC. Furthermore, we acquired the potential targets of miR-1 from datasets that transfected miR-1 into ccRCC cells, online prediction databases, differentially expressed genes from TCGA and literature...
December 2, 2017: Pathology, Research and Practice
Rui Zhang, Li-Jie Zhang, Mei-Ling Yang, Lan-Shan Huang, Gang Chen, Zhen-Bo Feng
The aims of the present study were to examine the potential role of microRNA‑233‑3p (miR)‑223‑3p in the tumorigenesis of hepatocellular carcinoma (HCC), and to investigate its diagnostic accuracy and potential molecular mechanisms. The expression data of miR‑223‑3p in HCC were obtained from the Gene Expression Omnibus (GEO). Data for the precursor miR‑223 were obtained from The Cancer Genome Atlas (TCGA). The diagnostic role of miR‑223‑3p was identified by the receiver operating curve (ROC), and the diagnostic value of miR‑223‑3p in HCC was calculated from qualified reports in the literature...
February 2018: Molecular Medicine Reports
Liang Liang, Li Gao, Xiao-Ping Zou, Meng-Lan Huang, Gang Chen, Jian-Jun Li, Xiao-Yong Cai
MicroRNA (miR)-338-5p has been studied in hepatocellular carcinoma (HCC); however, the diagnostic value and molecular mechanism underlying its actions remains to be elucidated. The present study aimed to validate the diagnostic ability of miR‑338‑5p and further explore the underlying molecular mechanism. Data from eligible studies, Gene Expression Omnibus (GEO) chips and The Cancer Genome Atlas (TCGA) datasets were gathered in the data mining and the integrated meta‑analysis, to evaluate the significance of miR‑338‑5p in diagnosing HCC comprehensively...
February 2018: Molecular Medicine Reports
B Xia, Y Li, J Zhou, B Tian, L Feng
OBJECTIVES: Osteoporosis is a chronic disease. The aim of this study was to identify key genes in osteoporosis. METHODS: Microarray data sets GSE56815 and GSE56814, comprising 67 osteoporosis blood samples and 62 control blood samples, were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified in osteoporosis using Limma package (3.2.1) and Meta-MA packages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify biological functions...
December 2017: Bone & Joint Research
David J Gregory, Igor Kramnik, Lester Kobzik
The goals of this study were to (a) define which host genes are of particular importance during the interactions between macrophages and intracellular pathogens, and (b) use this knowledge to gain fresh, experimental understanding of how macrophage activities may be manipulated during host defense. We designed an in silico method for meta-analysis of microarray gene expression data, and used this to combine data from 16 different studies of cells in the monocyte-macrophage lineage infected with seven different pathogens...
January 2018: FEBS Journal
Mattia Branca, Samuel Orso, Roberto C Molinari, Haotian Xu, Stéphane Guerrier, Yuming Zhang, Nabil Mili
Cutaneous melanoma is a highly aggressive skin cancer whose treatment and prognosis are critically affected by the presence of metastasis. In this study, we address the following issue: which gene transcripts and what kind of interactions between them can allow to predict nonmetastatic from metastatic melanomas with a high level of accuracy? We carry out a meta-analysis on the first gene expression set of the Leeds melanoma cohort, as made available online on 11 May 2016 through the ArrayExpress platform with MicroArray Gene Expression number 4725...
February 2018: Melanoma Research
Hai-Wei Liang, Xia Yang, Dong-Yue Wen, Li Gao, Xiang-Yu Zhang, Zhi-Hua Ye, Jie Luo, Zu-Yun Li, Yun He, Yu-Yan Pang, Gang Chen
Increasing evidence has demonstrated that microRNA (miR)‑133a‑3p is an important regulator of hepatocellular carcinoma (HCC). In the present study, the diagnostic role of miR‑133a‑3p in HCC, and the potential functional pathways, were both explored based on publicly available data. Eligible microarray datasets were collected from NCBI Gene Expression Omnibus (GEO) database and ArrayExpress database. The data related to HCC and matched adjacent normal tissues were also downloaded from The Cancer Genome Atlas (TCGA)...
January 2018: Molecular Medicine Reports
Harrison K Tsai, Jonathan Lehrer, Mohammed Alshalalfa, Nicholas Erho, Elai Davicioni, Tamara L Lotan
BACKGROUND: Neuroendocrine prostate cancer (NEPC) may be rising in prevalence as patients with advanced prostate cancer potentially develop resistance to contemporary anti-androgen treatment through a neuroendocrine phenotype. While prior studies comparing NEPC and prostatic adenocarcinoma have identified important candidates for targeted therapy, most have relied on few NEPC patients due to disease rarity, resulting in thousands of differentially expressed genes collectively and offering an opportunity for meta-analysis...
November 13, 2017: BMC Cancer
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