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Microarray gene expression meta-analysis

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https://www.readbyqxmd.com/read/27899990/microarray-analysis-of-differentially-expressed-genes-and-linker-genes-associated-with-the-molecular-mechanism-of-colorectal-cancer
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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...
October 15, 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
#9
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
#10
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
#11
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
#12
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
#13
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...
October 18, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27748342/functional-annotation-of-metastasis-associated-micrornas-of-melanoma-a-meta-analysis-of-expression-profiles
#14
Jing-Yi Li, Li-Li Zheng, Ting-Ting Wang, Min Hu
BACKGROUND: Melanoma is a type of cancer that develops from the pigment-containing cells. Until now, its pathological mechanisms remain largely unknown. The aim of this study was to identify metastasis-related microRNA (miRNAs) and gain an understanding of the biological functions in the metastasis of melanoma. METHODS: We searched the PubMed and Gene Expression Omnibus database to collect miRNA expression profiling datasets about melanoma, with key words of "melanoma", "miRNA", "microarray", and "gene expression profiling"...
2016: Chinese Medical Journal
https://www.readbyqxmd.com/read/27729915/a-systematic-view-of-the-mlo-family-in-rice-suggests-their-novel-roles-in-morphological-development-diurnal-responses-the-light-signaling-pathway-and-various-stress-responses
#15
Van N T Nguyen, Kieu T X Vo, Hyon Park, Jong-Seong Jeon, Ki-Hong Jung
The Mildew resistance Locus O (MLO) family is unique to plants, containing genes that were initially identified as a susceptibility factor to powdery mildew pathogens. However, little is known about the roles and functional diversity of this family in rice, a model crop plant. The rice genome has 12 potential MLO family members. To achieve systematic functional assignments, we performed a phylogenomic analysis by integrating meta-expression data obtained from public sources of microarray data and real-time expression data into a phylogenic tree...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27704359/transcriptomic-characterization-of-differential-gene-expression-in-oral-squamous-cell-carcinoma-a-meta-analysis-of-publicly-available-microarray-data-sets
#16
Yang Sun, Zhijian Sang, Qian Jiang, Xiaojun Ding, Youcheng Yu
Oral squamous cell carcinoma (OSCC) is a highly prevalent cancer worldwide, and OSCC often goes undiagnosed until advanced disease is present, which contributes to a low survival rate for OSCC patients. The identification of biomarkers for the early detection OSCC and novel therapeutic targets for OSCC treatment is an important research objective. We performed bioinformatics analyses of the gene expression profile of OSCC using microarray data to identify genes that contribute to the development of OSCC. We also predicted the transcription factors involved in the regulation of differential gene expression in OSCC...
October 4, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/27702671/major-differences-between-human-atopic-dermatitis-and-murine-models-as-determined-by-global-transcriptomic-profiling
#17
David A Ewald, Shinji Noda, Margeaux Oliva, Thomas Litman, Saeko Nakajima, Xuan Li, Hui Xu, Peter Scheipers, Naila Svitacheva, Tord Labuda, James G Krueger, Mayte Suárez-Fariñas, Kenji Kabashima, Emma Guttman-Yassky
BACKGROUND: Atopic dermatitis (AD) is caused by a complex interplay between immune and barrier abnormalities. Murine models of AD are essential for preclinical assessments of new treatments. While many models have been used to simulate AD, their transcriptomic profiles are not fully understood, and a comparison of these models with the human AD transcriptomic fingerprint is lacking. OBJECTIVE: We sought to evaluate the transcriptomic profiles of six common murine models and determine how they relate to human AD skin...
October 1, 2016: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/27625022/peripheral-blood-transcriptomic-signatures-of-fasting-glucose-and-insulin-concentrations
#18
Brian H Chen, Marie-France Hivert, Marjolein J Peters, Luke C Pilling, John D Hogan, Lisa M Pham, Lorna W Harries, Caroline S Fox, Stefania Bandinelli, Abbas Dehghan, Dena G Hernandez, Albert Hofman, Jaeyoung Hong, Roby Joehanes, Andrew D Johnson, Peter J Munson, Denis V Rybin, Andrew B Singleton, André G Uitterlinden, Saixia Ying, David Melzer, Daniel Levy, Joyce B J van Meurs, Luigi Ferrucci, Jose C Florez, Josée Dupuis, James B Meigs, Eric D Kolaczyk
Genome-wide association studies (GWAS) have successfully identified genetic loci associated with glycemic traits. However, characterizing the functional significance of these loci has proven challenging. We sought to gain insights into the regulation of fasting insulin and fasting glucose through the use of gene expression microarray data from peripheral blood samples of participants without diabetes in the Framingham Heart Study (FHS) (n = 5,056), the Rotterdam Study (RS) (n = 723), and the InCHIANTI Study (Invecchiare in Chianti) (n = 595)...
December 2016: Diabetes
https://www.readbyqxmd.com/read/27622044/large-scale-microarray-profiling-reveals-four-stages-of-immune-escape-in-non-hodgkin-lymphomas
#19
Marie Tosolini, Christelle Algans, Frédéric Pont, Bernard Ycart, Jean-Jacques Fournié
Non-Hodgkin B-cell lymphoma (B-NHL) are aggressive lymphoid malignancies that develop in patients due to oncogenic activation, chemo-resistance, and immune evasion. Tumor biopsies show that B-NHL frequently uses several immune escape strategies, which has hindered the development of checkpoint blockade immunotherapies in these diseases. To gain a better understanding of B-NHL immune editing, we hypothesized that the transcriptional hallmarks of immune escape associated with these diseases could be identified from the meta-analysis of large series of microarrays from B-NHL biopsies...
July 2016: Oncoimmunology
https://www.readbyqxmd.com/read/27613525/a-two-gene-prognostic-classifier-for-early-stage-lung-squamous-cell-carcinoma-in-multiple-large-scale-and-geographically-diverse-cohorts
#20
Rintaro Noro, Teruhide Ishigame, Naomi Walsh, Kouya Shiraishi, Ana I Robles, Bríd M Ryan, Aaron J Schetter, Elise D Bowman, Judith A Welsh, Masahiro Seike, Akihiko Gemma, Vidar Skaug, Steen Mollerup, Aage Haugen, Jun Yokota, Takashi Kohno, Curtis C Harris
INTRODUCTION: There are no validated molecular methods that prospectively identify patients with surgically resected lung squamous cell carcinoma (SCC) at high risk for recurrence. By focusing on the expression of genes with known functions in development of lung SCC and prognosis, we sought to develop a robust prognostic classifier of early-stage lung SCC. METHODS: The expression of 253 genes selected by literature search was evaluated in microarrays from 107 stage I/II tumors...
September 6, 2016: Journal of Thoracic Oncology
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