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Microarray gene expression meta-analysis

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https://www.readbyqxmd.com/read/28396836/down-regulation-of-mir-146a-5p-and-its-potential-targets-in-hepatocellular-carcinoma-validated-by-a-tcga-and-geo-based-study
#1
Xin Zhang, Zhi-Hua Ye, Hai-Wei Liang, Fang-Hui Ren, Ping Li, Yi-Wu Dang, Gang Chen
Our previous research has demonstrated that miR-146a-5p is down-regulated in hepatocellular carcinoma (HCC) and might play a tumor-suppressive role. In this study, we sought to validate the decreased expression with a larger cohort and to explore potential molecular mechanisms. GEO and TCGA databases were used to gather miR-146a-5p expression data in HCC, which included 762 HCC and 454 noncancerous liver tissues. A meta-analysis of the GEO-based microarrays, TCGA-based RNA-seq data, and additional qRT-PCR data validated the down-regulation of miR-146a-5p in HCC and no publication bias was observed...
April 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28347234/clinical-value-of-mir-145-5p-in-nsclc-and-potential-molecular-mechanism-exploration-a-retrospective-study-based-on-geo-qrt-pcr-and-tcga-data
#2
Ting-Qing Gan, Zu-Cheng Xie, Rui-Xue Tang, Tong-Tong Zhang, Dong-Yao Li, Zu-Yun Li, Gang Chen
MicroRNAs have been reported to be involved in various biological processes. Here, we performed a systematic analysis to explore the clinical value and potential molecular mechanism of miR-145-5p in non-small cell lung cancer. First, a meta-analysis was performed with eligible literature, followed by microRNA microarrays in the Gene Expression Omnibus database, to verify the diagnostic and prognostic values of miR-145-5p. A cohort of 125 clinical paired non-small cell lung cancer samples was next used to detect the level of miR-145-5p and to explore the relationship of miR-145-5p with clinicopathological parameters...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28335819/concordance-analysis-of-microarray-studies-identifies-representative-gene-expression-changes-in-parkinson-s-disease-a-comparison-of-33-human-and-animal-studies
#3
Erin Oerton, Andreas Bender
BACKGROUND: As the popularity of transcriptomic analysis has grown, the reported lack of concordance between different studies of the same condition has become a growing concern, raising questions as to the representativeness of different study types, such as non-human disease models or studies of surrogate tissues, to gene expression in the human condition. METHODS: In a comparison of 33 microarray studies of Parkinson's disease, correlation and clustering analyses were used to determine the factors influencing concordance between studies, including agreement between different tissue types, different microarray platforms, and between neurotoxic and genetic disease models and human Parkinson's disease...
March 23, 2017: BMC Neurology
https://www.readbyqxmd.com/read/28334340/meta-analytic-framework-for-liquid-association
#4
Lin Wang, Silvia Liu, Ying Ding, Shin-Sheng Yuan, Yen-Yi Ho, George C Tseng
Motivation: Although coexpression analysis via pair-wise expression correlation is popularly used to elucidate gene-gene interactions at the whole-genome scale, many complicated multi-gene regulations require more advanced detection methods. Liquid association is a powerful tool to detect the dynamic correlation of two gene variables depending on the expression level of a third variable (LA scouting gene). Liquid association detection from single transcriptomic study, however, is often unstable and not generalizable due to cohort bias, biological variation, and limited sample size...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28320358/preservation-affinity-in-consensus-modules-among-stages-of-hiv-1-progression
#5
Sk Md Mosaddek Hossain, Sumanta Ray, Anirban Mukhopadhyay
BACKGROUND: Analysis of gene expression data provides valuable insights into disease mechanism. Investigating relationship among co-expression modules of different stages is a meaningful tool to understand the way in which a disease progresses. Identifying topological preservation of modular structure also contributes to that understanding. METHODS: HIV-1 disease provides a well-documented progression pattern through three stages of infection: acute, chronic and non-progressor...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28295046/transcriptomic-immaturity-of-the-hippocampus-and-prefrontal-cortex-in-patients-with-alcoholism
#6
Tomoyuki Murano, Hisatsugu Koshimizu, Hideo Hagihara, Tsuyoshi Miyakawa
Alcoholism, which is defined as the recurring harmful use of alcohol despite its negative consequences, has a lifetime prevalence of 17.8%. Previous studies have shown that chronic alcohol consumption disrupts various brain functions and behaviours. However, the precise mechanisms that underlie alcoholism are currently unclear. Recently, we discovered "pseudo-immature" brain cell states of the dentate gyrus and prefrontal cortex (PFC) in mouse models of psychotic disorders and epileptic seizure. Similar pseudo-immaturity has been observed in patients with psychotic disorders, such as schizophrenia and bipolar disorder...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28286608/meta-analysis-of-gene-expression-profiles-in-acute-promyelocytic-leukemia-reveals-involved-pathways
#7
Mahdi Jalili, Ali Salehzadeh-Yazdi, Saeed Mohammadi, Marjan Yaghmaie, Ardeshir Ghavamzadeh, Kamran Alimoghaddam
Background: Acute promyelocytic leukemia (APL) is a unique subtype of acute leukemia. APL is a curable disease; however, drug resistance, early mortality, disease relapse and treatment-related complications remain challenges in APL patient management. One issue underlying these challenges is that the molecular mechanisms of the disease are not sufficiently understood. Materials and Methods: In this study, we performed a meta-analysis of gene expression profiles derived from microarray experiments and explored the background of disease by functional and pathway analysis...
January 1, 2017: International Journal of Hematology-oncology and Stem Cell Research
https://www.readbyqxmd.com/read/28272699/alteration-of-endothelial-nitric-oxide-synthase-expression-in-acute-pulmonary-embolism-a-study-from-bench-to-bioinformatics
#8
R Miao, D Leng, M Liu, X-X Huang, J-F Li, J-N Gong, Y Liang, Z-G Zhai, Y-H Yang, Y Wang, J Wan
OBJECTIVE: This study sought to explore endothelial nitric oxide synthase (eNOS) expression in acute pulmonary thromboembolism (APE). MATERIALS AND METHODS: eNOS expression in lung tissue and bone marrow-derived endothelial progenitor cells (BM-EPCs) from APE mouse models was assessed by immunohistochemistry and real-time PCR. A gene expression profile meta-analysis was performed on human venous thromboembolism (VTE) whole blood samples recorded in the Gene Expression Omnibus (GEO) repository...
February 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28251349/prognostic-significance-of-interferon-regulating-factor-4-irf4-in-node-negative-breast-cancer
#9
Anne-Sophie Heimes, K Madjar, K Edlund, M J Battista, K Almstedt, S Gebhard, S Foersch, J Rahnenführer, W Brenner, A Hasenburg, J G Hengstler, M Schmidt
PURPOSE: The transcription factor IRF4 regulates immunoglobulin class switch recombination as well as plasma cell differentiation. We examined the prognostic significance of IRF4 expression in node-negative breast cancer (BC). METHODS: IRF4 expression was evaluated by immunostaining in a cohort of 197 node-negative BC patients not treated in adjuvant setting, referred to as Mainz cohort. The prognostic significance of immunohistochemically determined IRF4 expression for metastasis-free survival (MFS) was examined by Kaplan-Meier survival analysis as well as univariate and multivariate Cox analysis adjusted for age, pT stage, histological grade, ER, and HER2 status...
March 1, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28222515/meta-analysis-of-parkinson-s-disease-and-alzheimer-s-disease-revealed-commonly-impaired-pathways-and-dysregulation-of-nrf2-dependent-genes
#10
Qian Wang, Wen-Xing Li, Shao-Xing Dai, Yi-Cheng Guo, Fei-Fei Han, Jun-Juan Zheng, Gong-Hua Li, Jing-Fei Huang
Many lines of evidence suggest that Parkinson's disease (PD) and Alzheimer's disease (AD) have common characteristics, such as mitochondrial dysfunction and oxidative stress. As the underlying molecular mechanisms are unclear, we perform a meta-analysis with 9 microarray datasets of PD studies and 7 of AD studies to explore it. Functional enrichment analysis revealed that PD and AD both showed dysfunction in the synaptic vesicle cycle, GABAergic synapses, phagosomes, oxidative phosphorylation, and TCA cycle pathways, and AD had more enriched genes...
2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28218403/unveiling-gene-trait-relationship-by-cross-platform-meta-analysis-on-chinese-hamster-ovary-cell-transcriptome
#11
Liang Zhao, Hsu-Yuan Fu, Ravali Raju, Nandita Vishwanathan, Wei-Shou Hu
In the past few years, transcriptome analysis has been increasingly employed to better understand the physiology of Chinese hamster ovary (CHO) cells at a global level. As more transcriptome data accumulated, meta-analysis on data sets collected from various sources can potentially provide better insights on common properties of those cells. Here, we performed meta-analysis on transcriptome data of different CHO cell lines obtained using NimbleGen or Affymetrix microarray platforms. Hierarchical clustering, non-negative matrix factorization (NMF) analysis, and principal component analysis (PCA) accordantly showed the samples were clustered into two groups: one consists of adherent cells in serum-containing medium, and the other suspension cells in serum-free medium...
February 20, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28183295/meta-analysis-of-gene-expression-in-relapsed-childhood-b-acute-lymphoblastic-leukemia
#12
Yock-Ping Chow, Hamidah Alias, Rahman Jamal
BACKGROUND: Relapsed pediatric B-acute lymphoblastic leukemia (B-ALL) remains as the leading cause of cancer death among children. Other than stem cell transplantation and intensified chemotherapy, no other improved treatment strategies have been approved clinically. Gene expression profiling represents a powerful approach to identify potential biomarkers and new therapeutic targets for various diseases including leukemias. However, inadequate sample size in many individual experiments has failed to provide adequate study power to yield translatable findings...
February 10, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28158196/transcriptome-wide-co-expression-analysis-identifies-lrrc2-as-a-novel-mediator-of-mitochondrial-and-cardiac-function
#13
Chris McDermott-Roe, Marion Leleu, Glenn C Rowe, Oleg Palygin, John D Bukowy, Judy Kuo, Monika Rech, Steffie Hermans-Beijnsberger, Sebastian Schaefer, Eleonora Adami, Esther E Creemers, Matthias Heinig, Blanche Schroen, Zoltan Arany, Enrico Petretto, Aron M Geurts
Mitochondrial dysfunction contributes to myriad monogenic and complex pathologies. To understand the underlying mechanisms, it is essential to define the full complement of proteins that modulate mitochondrial function. To identify such proteins, we performed a meta-analysis of publicly available gene expression data. Gene co-expression analysis of a large and heterogeneous compendium of microarray data nominated a sub-population of transcripts that whilst highly correlated with known mitochondrial protein-encoding transcripts (MPETs), are not themselves recognized as generating proteins either localized to the mitochondrion or pertinent to functions therein...
2017: PloS One
https://www.readbyqxmd.com/read/28152520/clinical-significance-and-effect-of-aeg-1-on-the-proliferation-invasion-and-migration-of-nsclc-a-study-based-on-immunohistochemistry-tcga-bioinformatics-in-vitro-and-in-vivo-verification
#14
Yu Zhang, Zu-Yun Li, Xin-Xi Hou, Xiao Wang, Yi-Huan Luo, Yan-Ping Ying, Gang Chen
BACKGROUND: Astrocyte elevated gene-1 (AEG-1) is related to the tumorigenesis and deterioration of different cancers, including non-small cell lung cancer (NSCLC). However, the effect of AEG-1 in NSCLC remains unclear. In this study, we aimed to investigate the clinical significance and effect of AEG-1 on biological function of NSCLC. RESULTS: AEG-1 was significantly overexpressed in NSCLC tissues and closely correlated to the deterioration of NSCLC based on tissue microarray, TCGA database and meta-analysis...
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28151718/the-prognostic-role-of-androgen-receptor-in-patients-with-early-stage-breast-cancer-a-meta-analysis-of-clinical-and-gene-expression-data
#15
Ivana Bozovic-Spasojevic, Dimitrios Zardavas, Sylvain Brohée, Lieveke Ameye, Debora Fumagalli, Felipe Ades, Evandro De Azambuja, Yacine Bareche, Martine Piccart, Marianne Paesmans, Christos Sotiriou
Androgen receptor (AR) expression has been observed in about 70% of breast cancer (BC) patients, but its prognostic role remains uncertain. METHODS: To assess the prognostic role of AR expression in early-stage BC we performed a meta-analysis of studies that evaluated the impact of AR at the protein and gene expression level on disease free survival (DFS) and/or overall survival (OS). Eligible studies were identified by systematic review of electronic databases using the MeSH-terms "breast neoplasm" and "androgen receptor" and were selected after a qualitative assessment based on the REMARK criteria...
November 9, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28149325/meta-analytic-support-vector-machine-for-integrating-multiple-omics-data
#16
SungHwan Kim, Jae-Hwan Jhong, JungJun Lee, Ja-Yong Koo
BACKGROUND: Of late, high-throughput microarray and sequencing data have been extensively used to monitor biomarkers and biological processes related to many diseases. Under this circumstance, the support vector machine (SVM) has been popularly used and been successful for gene selection in many applications. Despite surpassing benefits of the SVMs, single data analysis using small- and mid-size of data inevitably runs into the problem of low reproducibility and statistical power. To address this problem, we propose a meta-analytic support vector machine (Meta-SVM) that can accommodate multiple omics data, making it possible to detect consensus genes associated with diseases across studies...
2017: BioData Mining
https://www.readbyqxmd.com/read/28122634/integrated-genome-wide-analysis-of-expression-quantitative-trait-loci-aids-interpretation-of-genomic-association-studies
#17
Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Sai-Xia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael L Feolo, Nataliya R Sharopova, Anne Sturcke, Alejandro A Schäffer, Nancy Heard-Costa, Han Chen, Po-Ching Liu, Richard Wang, Kimberly A Woodhouse, Kahraman Tanriverdi, Jane E Freedman, Nalini Raghavachari, Josée Dupuis, Andrew D Johnson, Christopher J O'Donnell, Daniel Levy, Peter J Munson
BACKGROUND: Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenotype-associated SNPs in genome-wide association studies (GWAS). The small sample sizes of some previous eQTL studies have limited their statistical power. We conducted an eQTL investigation of microarray-based gene and exon expression levels in whole blood in a cohort of 5257 individuals, exceeding the single cohort size of previous studies by more than a factor of 2...
January 25, 2017: Genome Biology
https://www.readbyqxmd.com/read/28108623/tumor-induced-stromal-stat1-accelerates-breast-cancer-via-deregulating-tissue-homeostasis
#18
Victoria R Zellmer, Patricia M Schnepp, Sarah L Fracci, Xuejuan Tan, Erin N Howe, Siyuan Zhang
The tumor microenvironment (TME) is a dynamic tissue space in which the tumor exists, plays a significant role in tumor initiation, and is a key contributor in cancer progression; however, little is known about tumor-induced changes in the adjacent tissue stroma. Herein, tumor-induced changes in the TME were explored at the morphological and molecular level to further understand cancer progression. Tumor-adjacent mammary glands (TAGs) displayed altered branching morphology, expansion of myofibroblasts, and increased mammosphere formation, broadly suggesting a tumor-induced field effect...
January 20, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28102354/a-signature-of-renal-stress-resistance-induced-by-short-term-dietary-restriction-fasting-and-protein-restriction
#19
F Jongbloed, T C Saat, M Verweij, C Payan-Gomez, J H J Hoeijmakers, S van den Engel, C T van Oostrom, G Ambagtsheer, S Imholz, J L A Pennings, H van Steeg, J N M IJzermans, M E T Dollé, R W F de Bruin
During kidney transplantation, ischemia-reperfusion injury (IRI) induces oxidative stress. Short-term preoperative 30% dietary restriction (DR) and 3-day fasting protect against renal IRI. We investigated the contribution of macronutrients to this protection on both phenotypical and transcriptional levels. Male C57BL/6 mice were fed control food ad libitum, underwent two weeks of 30%DR, 3-day fasting, or received a protein-, carbohydrate- or fat-free diet for various periods of time. After completion of each diet, renal gene expression was investigated using microarrays...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28060761/identification-of-micrornas-associated-with-glioma-diagnosis-and-prognosis
#20
Xinyun Ye, Wenjin Wei, Zhengyu Zhang, Chunming He, Ruijin Yang, Jinshi Zhang, Zhiwu Wu, Qianliang Huang, Qiuhua Jiang
The sensitivity and specificity of microRNAs (miRNAs) for diagnosing glioma are controversial. We therefore performed a meta-analysis to systematically identify glioma-associated miRNAs. We initially screened five miRNA microarray datasets to evaluate the differential expression of miRNAs between glioma and normal tissues. We next compared the expression of the miRNAs in different organs and tissues to assess the sensitivity and specificity of the differentially expressed miRNAs in the diagnosis of glioma. Finally, pathway analysis was performed using GeneGO...
January 2, 2017: Oncotarget
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