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Microarray gene expression meta-analysis

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https://www.readbyqxmd.com/read/28102354/a-signature-of-renal-stress-resistance-induced-by-short-term-dietary-restriction-fasting-and-protein-restriction
#1
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
#2
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
https://www.readbyqxmd.com/read/28036281/the-prognostic-value-of-long-noncoding-rna-hottip-on-clinical-outcomes-in-breast-cancer
#3
Yinlong Yang, Jinxian Qian, Youqun Xiang, Yizuo Chen, Jinmiao Qu
Although a few studies have assessed the prognostic value of long noncoding RNA HOTTIP in patients with malignant tumors, the relationship between HOTTIP and clinical outcome of breast cancer remains elusive. The aim of this study is to explore the prognostic significance of HOTTIP in breast cancer patients. A meta-analysis was performed to involve the eligible studies to investigate the association of HOTTIP expression level with outcome in cancer patients. Pooled hazard ratios (HRs) and 95% confidence interval (CI) of HOTTIP for cancer survival were calculated...
December 27, 2016: Oncotarget
https://www.readbyqxmd.com/read/28033256/identified-molecular-mechanism-of-interaction-between-environmental-risk-factors-and-differential-expression-genes-in-cartilage-of-kashin-beck-disease
#4
Fang-Fang Yu, Yan-Xiang Zhang, Lian-He Zhang, Wen-Rong Li, Xiong Guo, Mikko J Lammi
As environmental risk factors (ERFs) play an important role in the pathogenesis of Kashin-Beck disease (KBD), it is important to identify the interaction between ERFs and differentially expression genes (DEGs) in KBD. The environmental response genes (ERGs) were analyzed in cartilage of KBD in comparison to normal controls.We searched 5 English and 3 Chinese databases from inception to September 2015, to identify case-control studies that examined ERFs for KBD using integrative meta-analysis and systematic review...
December 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27997581/identification-of-polycystic-ovary-syndrome-pcos-specific-genes-in-cumulus-and-mural-granulosa-cells
#5
Alp Aydos, Aykut Gurel, Yasemin Oztemur Islakoglu, Senem Noyan, Bagdagul Gokce, Tolga Ecemis, Cemil Kaya, Arif Tarik Aksu, Bala Gur Dedeoglu
Polycystic ovary syndrome (PCOS) is a metabolic and endocrine disorder which affects women of reproductive age with prevalence of 8-18%. The oocyte within the follicle is surrounded by cumulus cells (CCs), which connect with mural granulosa cells (MGCs) that are responsible for secreting steroid hormones. The main aim of this study is comparing gene expression profiles of MGCs and CCs in PCOS and control samples to identify PCOS-specific differentially expressed genes (DEGs). In this study, two microarray databases were searched for mRNA expression microarray studies performed with CCs and MGCs obtained from PCOS patients and control samples...
2016: PloS One
https://www.readbyqxmd.com/read/27989982/meta-analysis-of-microarray-based-expression-profiles-to-identify-differentially-expressed-genes-in-intracranial-aneurysms
#6
Zhe Xu, Hao Li, Jiangman Song, Bing Han, Zheng Wang, Yong Cao, Shuo Wang, Jizong Zhao
OBJECTIVE: To gain comprehensive insight into the molecular mechanism of formation and rupture of intracranial aneurysms (IAs). METHODS: All the publicly accessible microarray-based whole-genome gene expression profiles on IAs were retrieved. The significance analysis of microarrays method was applied to identify differentially expressed genes (DEGs). Functional annotation was performed using gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses...
October 27, 2016: World Neurosurgery
https://www.readbyqxmd.com/read/27939925/a-candidate-regulatory-variant-at-the-trem-gene-cluster-associates-with-decreased-alzheimer-s-disease-risk-and-increased-treml1-and-trem2-brain-gene-expression
#7
Minerva M Carrasquillo, Mariet Allen, Jeremy D Burgess, Xue Wang, Samantha L Strickland, Shivani Aryal, Joanna Siuda, Michaela L Kachadoorian, Christopher Medway, Curtis S Younkin, Asha Nair, Chen Wang, Pritha Chanana, Daniel Serie, Thuy Nguyen, Sarah Lincoln, Kimberly G Malphrus, Kevin Morgan, Todd E Golde, Nathan D Price, Charles C White, Philip L De Jager, David A Bennett, Yan W Asmann, Julia E Crook, Ronald C Petersen, Neill R Graff-Radford, Dennis W Dickson, Steven G Younkin, Nilüfer Ertekin-Taner
INTRODUCTION: We hypothesized that common Alzheimer's disease (AD)-associated variants within the triggering receptor expressed on myeloid (TREM) gene cluster influence disease through gene expression. METHODS: Expression microarrays on temporal cortex and cerebellum from ∼400 neuropathologically diagnosed subjects and two independent RNAseq replication cohorts were used for expression quantitative trait locus analysis. RESULTS: A variant within a DNase hypersensitive site 5' of TREM2, rs9357347-C, associates with reduced AD risk and increased TREML1 and TREM2 levels (uncorrected P = 6...
December 8, 2016: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/27899990/microarray-analysis-of-differentially-expressed-genes-and-linker-genes-associated-with-the-molecular-mechanism-of-colorectal-cancer
#8
Xingjie Shen, Meng Yue, Fansheng Meng, Jingyu Zhu, Xiaoyan Zhu, Yakun Jiang
Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide and remains the third leading cause of cancer-associated mortality. The present study aimed to fully elucidate the pathogenesis of CRC and identify associated genes in tumor development. Microarray GSE44076, GSE41328 and GSE44861 datasets were downloaded from the Gene Expression Omnibus database and integrated with meta-analysis. Differentially-expressed genes (DEGs) were identified from CRC samples compared with adjacent non-cancerous controls using the Limma package in R, followed by functional analysis using the Database for Annotation, Visualization, and Integrated Discovery online tool...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27892526/comprehensive-gene-expression-meta-analysis-and-integrated-bioinformatic-approaches-reveal-shared-signatures-between-thrombosis-and-myeloproliferative-disorders
#9
Prabhash Kumar Jha, Aatira Vijay, Anita Sahu, Mohammad Zahid Ashraf
Thrombosis is a leading cause of morbidity and mortality in patients with myeloproliferative disorders (MPDs), particularly polycythemia vera (PV) and essential thrombocythemia (ET). Despite the attempts to establish a link between them, the shared biological mechanisms are yet to be characterized. An integrated gene expression meta-analysis of five independent publicly available microarray data of the three diseases was conducted to identify shared gene expression signatures and overlapping biological processes...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27862943/blood-transcriptomic-comparison-of-individuals-with-and-without-autism-spectrum-disorder-a-combined-samples-mega-analysis
#10
Daniel S Tylee, Jonathan L Hess, Thomas P Quinn, Rahul Barve, Hailiang Huang, Yanli Zhang-James, Jeffrey Chang, Boryana S Stamova, Frank R Sharp, Irva Hertz-Picciotto, Stephen V Faraone, Sek Won Kong, Stephen J Glatt
Blood-based microarray studies comparing individuals affected with autism spectrum disorder (ASD) and typically developing individuals help characterize differences in circulating immune cell functions and offer potential biomarker signal. We sought to combine the subject-level data from previously published studies by mega-analysis to increase the statistical power. We identified studies that compared ex vivo blood or lymphocytes from ASD-affected individuals and unrelated comparison subjects using Affymetrix or Illumina array platforms...
November 11, 2016: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/27846842/a-meta-analysis-of-public-microarray-data-identifies-gene-regulatory-pathways-deregulated-in-peripheral-blood-mononuclear-cells-from-individuals-with-systemic-lupus-erythematosus-compared-to-those-without
#11
Wendy Kröger, Darlington Mapiye, Jean-Baka Domelevo Entfellner, Nicki Tiffin
BACKGROUND: Systemic Lupus Erythematosus (SLE) is a complex, multi-systemic, autoimmune disease for which the underlying aetiological mechanisms are poorly understood. The genetic and molecular processes underlying lupus have been extensively investigated using a variety of -omics approaches, including genome-wide association studies, candidate gene studies and microarray experiments of differential gene expression in lupus samples compared to controls. METHODS: This study analyses a combination of existing microarray data sets to identify differentially regulated genetic pathways that are dysregulated in human peripheral blood mononuclear cells from SLE patients compared to unaffected controls...
November 15, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27835655/a-transcriptome-meta-analysis-proposes-novel-biological-roles-for-the-antifungal-protein-anafp-in-aspergillus-niger
#12
Norman Paege, Sascha Jung, Paul Schäpe, Dirk Müller-Hagen, Jean-Paul Ouedraogo, Caroline Heiderich, Johanna Jedamzick, Benjamin M Nitsche, Cees A van den Hondel, Arthur F Ram, Vera Meyer
Understanding the genetic, molecular and evolutionary basis of cysteine-stabilized antifungal proteins (AFPs) from fungi is important for understanding whether their function is mainly defensive or associated with fungal growth and development. In the current study, a transcriptome meta-analysis of the Aspergillus niger γ-core protein AnAFP was performed to explore co-expressed genes and pathways, based on independent expression profiling microarrays covering 155 distinct cultivation conditions. This analysis uncovered that anafp displays a highly coordinated temporal and spatial transcriptional profile which is concomitant with key nutritional and developmental processes...
2016: PloS One
https://www.readbyqxmd.com/read/27830726/meta-analysis-of-gene-expression-studies-in-endometrial-cancer-identifies-gene-expression-profiles-associated-with-aggressive-disease-and-patient-outcome
#13
Tracy A O'Mara, Min Zhao, Amanda B Spurdle
Although endometrioid endometrial cancer (EEC; comprising ~80% of all endometrial cancers diagnosed) is typically associated with favourable patient outcome, a significant portion (~20%) of women with this subtype will relapse. We hypothesised that gene expression predictors of the more aggressive non-endometrioid endometrial cancers (NEEC) could be used to predict EEC patients with poor prognosis. To explore this hypothesis, we performed meta-analysis of 12 gene expression microarray studies followed by validation using RNA-Seq data from The Cancer Genome Atlas (TCGA) and identified 1,253 genes differentially expressed between EEC and NEEC...
November 10, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27824868/drug-repositioning-through-systematic-mining-of-gene-coexpression-networks-in-cancer
#14
Alexander E Ivliev, Peter A C 't Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G Sergeeva
Gene coexpression network analysis is a powerful "data-driven" approach essential for understanding cancer biology and mechanisms of tumor development. Yet, despite the completion of thousands of studies on cancer gene expression, there have been few attempts to normalize and integrate co-expression data from scattered sources in a concise "meta-analysis" framework. We generated such a resource by exploring gene coexpression networks in 82 microarray datasets from 9 major human cancer types. The analysis was conducted using an elaborate weighted gene coexpression network (WGCNA) methodology and identified over 3,000 robust gene coexpression modules...
2016: PloS One
https://www.readbyqxmd.com/read/27816808/talin-and-vinculin-are-downregulated-in-atherosclerotic-plaque-tampere-vascular-study
#15
Magdaléna von Essen, Rolle Rahikainen, Niku Oksala, Emma Raitoharju, Ilkka Seppälä, Ari Mennander, Thanos Sioris, Ivana Kholová, Norman Klopp, Thomas Illig, Pekka J Karhunen, Mika Kähönen, Terho Lehtimäki, Vesa P Hytönen
BACKGROUND AND AIMS: Focal adhesions (FA) play an important role in the tissue remodeling and in the maintenance of tissue integrity and homeostasis. Talin and vinculin proteins are among the major constituents of FAs contributing to cellular well-being and intercellular communication. METHODS: Microarray analysis (MA) and qRT-PCR low-density array were implemented to analyze talin-1, talin-2, meta-vinculin and vinculin gene expression in circulating blood and arterial plaque...
December 2016: Atherosclerosis
https://www.readbyqxmd.com/read/27803687/emerging-putative-associations-between-non-coding-rnas-and-protein-coding-genes-in-neuropathic-pain-added-value-from-reusing-microarray-data
#16
Hemalatha B Raju, Nicholas F Tsinoremas, Enrico Capobianco
Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN...
2016: Frontiers in Neurology
https://www.readbyqxmd.com/read/27790248/large-scale-gene-expression-meta-analysis-reveals-tissue-specific-sex-biased-gene-expression-in-humans
#17
Benjamin T Mayne, Tina Bianco-Miotto, Sam Buckberry, James Breen, Vicki Clifton, Cheryl Shoubridge, Claire T Roberts
The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analyzed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27785066/biomarker-discovery-to-improve-prediction-of-breast-cancer-survival-using-gene-expression-profiling-meta-analysis-and-tissue-validation
#18
Liwei Meng, Yingchun Xu, Chaoyang Xu, Wei Zhang
PURPOSE: Breast cancer is the leading cause of cancer death worldwide in women. The molecular mechanism for human breast cancer is unknown. Gene microarray has been widely used in breast cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis survival. So far, the valuable multigene signatures in clinical practice are unclear, and the biological importance of individual genes is difficult to detect, as the described signatures virtually do not overlap...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27769251/klhl21-a-novel-gene-that-contributes-to-the-progression-of-hepatocellular-carcinoma
#19
Lei Shi, Wenfa Zhang, Fagui Zou, Lihua Mei, Gang Wu, Yong Teng
BACKGROUND: Hepatocellular carcinoma (HCC) has very high prevalence and associated-mortality. However, targeted therapies that are currently used in clinical practice for HCC have certain limitations, in part because of the lack of reliable and clinically applicable biomarkers that can be used for diagnosis and prognosis assessments and for the surveillance of treatment effectiveness. METHODS: Meta-analysis was used to analyze the integrated microarray data for global identification of a set of robust biomarkers for HCC...
October 21, 2016: BMC Cancer
https://www.readbyqxmd.com/read/27753529/cyclin-g2-promotes-cell-cycle-arrest-in-breast-cancer-cells-responding-to-fulvestrant-and-metformin-and-correlates-with-patient-survival
#20
Maike Zimmermann, Aruni P S Arachchige-Don, Michaela S Donaldson, Tommaso Patriarchi, Mary C Horne
Definition of cell cycle control proteins that modify tumor cell resistance to estrogen (E2) signaling antagonists could inform clinical choice for estrogen receptor positive (ER+) breast cancer (BC) therapy. Cyclin G2 (CycG2) is upregulated during cell cycle arrest responses to cellular stresses and growth inhibitory signals and its gene, CCNG2, is directly repressed by E2-bound ER complexes. Our previous studies showed that blockade of HER2, PI3K and mTOR signaling upregulates CycG2 expression in HER2+ BC cells, and that CycG2 overexpression induces cell cycle arrest...
December 2016: Cell Cycle
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