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gene expression meta-analysis

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https://www.readbyqxmd.com/read/28938655/prognostic-value-of-decreased-long-non-coding-rna-tusc7-expression-in-some-solid-tumors-a-systematic-review-and-meta-analysis
#1
Na Li, Meilan Yang, Ke Shi, Wei Li
Accumulating evidences indicated that tumor suppressor candidate 7 (TUSC7) is a putatively tumor suppressor gene in various tumors. We carried out current systematic review and meta-analysis to explore the decreased expression of TUSC7 associate with prognostic and clinicopathological characteristic in cancer patients. A literature collection search in the online electronic databases PubMed, Embase, Web of Science, and CNKI was conducted to obtain eligible studies (up to February 20, 2017). A total of nine studies comprise 757 patients were identified and included in present meta-analysis based on the selection and inclusion criteria...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28937020/unique-characteristics-of-arid1a-mutation-and-protein-level-in-gastric-and-colorectal-cancer-a-meta-analysis
#2
REVIEW
Young-Sik Kim, Hoiseon Jeong, Jung-Woo Choi, Hwa Eun Oh, Ju-Han Lee
BACKGROUND/AIM: Recently, AT-rich interactive domain-containing 1A protein (ARID1A) has been identified as a novel tumor suppressor gene in gastric cancer (GC) and colorectal cancer (CRC). However, the clinicopathologic value of ARID1A mutation or protein level in GC and CRC patients is controversial. Hence, we conducted a meta-analysis on the relationship between ARID1A aberrations and clinicopathologic parameters in GC and CRC. MATERIALS AND METHODS: Relevant published studies were selected from PubMed and EMBASE...
September 2017: Saudi Journal of Gastroenterology: Official Journal of the Saudi Gastroenterology Association
https://www.readbyqxmd.com/read/28934396/evaluation-of-shared-genetic-aetiology-between-osteoarthritis-and-bone-mineral-density-identifies-smad3-as-a-novel-osteoarthritis-risk-locus
#3
Sophie Hackinger, Katerina Trajanoska, Unnur Styrkarsdottir, Eleni Zengini, Julia Steinberg, Graham R S Ritchie, Konstantinos Hatzikotoulas, Arthur Gilly, Evangelos Evangelou, John P Kemp, David Evans, Thorvaldur Ingvarsson, Helgi Jonsson, Unnur Thorsteinsdottir, Kari Stefansson, Andrew W McCaskie, Roger A Brooks, Jeremy M Wilkinson, Fernando Rivadeneira, Eleftheria Zeggini
Osteoarthritis (OA) is a common complex disease with high public health burden and no curative therapy. High bone mineral density (BMD) is associated with an increased risk of developing OA, suggesting a shared underlying biology. Here, we performed the first systematic overlap analysis of OA and BMD on a genome wide scale. We used summary statistics from the GEFOS consortium for lumbar spine (n = 31,800) and femoral neck (n = 32,961) BMD, and from the arcOGEN consortium for three OA phenotypes (hip, ncases=3,498; knee, ncases=3,266; hip and/or knee, ncases=7,410; ncontrols=11,009)...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28933415/integrative-systems-biology-investigation-of-fabry-disease
#4
Marco Fernandes, Holger Husi
Fabry disease (FD) is a rare X-linked recessive genetic disorder caused by a deficient activity of the lysosomal enzyme alpha-galactosidase A (GLA) and is characterised by intra-lysosomal accumulation of globotriaosylceramide (Gb3). We performed a meta-analysis of peer-reviewed publications including high-throughput omics technologies including naïve patients and those undergoing enzyme replacement therapy (ERT). This study describes FD on a systems level using a systems biology approach, in which molecular data sourced from multi-omics studies is extracted from the literature and integrated as a whole in order to reveal the biochemical processes and molecular pathways potentially affected by the dysregulation of differentially expressed molecules...
November 15, 2016: Diseases (Basel)
https://www.readbyqxmd.com/read/28932563/a-systematic-and-genome-wide-correlation-meta-analysis-of-pd-l1-expression-and-targetable-nsclc-driver-genes
#5
Jin Li, Yaoqi Chen, Xiaoshun Shi, Xiaobing Le, Fenglan Feng, Jingyi Chen, Chengzhi Zhou, Yusong Chen, Shuai Wen, Haikang Zeng, Allen M Chen, Yu Zhang
BACKGROUND: Studies have shown that the ligand of programmed cell death protein 1 (B7-H1, CD274 or PD-L1) is related to lung cancer driver genes. Although studies have examined the association between lung cancer driver gene mutations or expression and PD-L1 expression, the present studies have not been mined the correlation systematically and genome-widely. METHODS: All relevant published PD-L1 articles with driver genes data and the RNA-seq dataset from The Cancer Genome Atlas (TCGA) were analyzed...
August 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28930859/p16-methylation-was-associated-with-the-development-age-hepatic-viruses-infection-of-hepatocellular-carcinoma-and-p16-expression-had-a-poor-survival-a-systematic-meta-analysis-prisma
#6
Xueyou Lv, Guoliang Ye, Xinjun Zhang, Tao Huang
BACKGROUND: Loss of tumor suppressor gene p16 expression via promoter methylation has been reported in hepatocellular carcinoma (HCC). This meta-analysis was conducted to evaluate the correlation between p16 methylation and HCC. Additionally, we also analyzed the potential prognostic role of p16 methylation, expression or alteration-associated HCC. METHODS: Online databases based on the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guideline were performed to analyze the role of p16 gene in HCC...
September 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28927412/analysis-of-microrna-mirna-expression-profiles-reveals-11-key-biomarkers-associated-with-non-small-cell-lung-cancer
#7
Ke Wang, Mingwei Chen, Wei Wu
BACKGROUND: Non-small cell lung cancer (NSCLC) accounts for more than 85% of lung cancer cases which cause most of cancer-related deaths globally. However, the results vary largely in different studies due to different platforms and sample sizes. Here, we aim to identify the key miRNAs in the carcinogenesis of NSCLC that might be potential biomarkers for this cancer. METHODS: Meta-analysis was performed on miRNA profile using seven datasets of NSCLC studies. Furthermore, we predicted and investigated the functions of genes regulated by key miRNAs...
September 19, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28925997/precision-annotation-of-digital-samples-in-ncbi-s-gene-expression-omnibus
#8
Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D Azad, Mohamad O Hadied, Shuaib Raza, Benjamin Abhishek Rayikanti, Bin Chen, Hyojung Paik, Dvir Aran, Jordan Spatz, Daniel Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A Musen, Atul J Butte
The Gene Expression Omnibus (GEO) contains more than two million digital samples from functional genomics experiments amassed over almost two decades. However, individual sample meta-data remains poorly described by unstructured free text attributes preventing its largescale reanalysis. We introduce the Search Tag Analyze Resource for GEO as a web application (http://STARGEO.org) to curate better annotations of sample phenotypes uniformly across different studies, and to use these sample annotations to define robust genomic signatures of disease pathology by meta-analysis...
September 19, 2017: Scientific Data
https://www.readbyqxmd.com/read/28924174/gene-expression-meta-analysis-in-diffuse-low-grade-glioma-and-the-corresponding-histological-subtypes
#9
Siqi Wang, Feng Jin, Wenliang Fan, Fang Liu, Yan Zou, Xuehan Hu, Haibo Xu, Ping Han
Diffuse low-grade glioma (DLGG) is a well-differentiated, slow-growing tumour with an inherent tendency to progress to high-grade glioma. The potential roles of genetic alterations in DLGG development have not yet been fully delineated. Therefore, the current study performed an integrated gene expression meta-analysis of eight independent, publicly available microarray datasets including 291 DLGGs and 83 non-glioma (NG) samples to identify gene expression signatures associated with DLGG. Using INMEX, 708 differentially expressed genes (DEGs) (385 upregulated and 323 downregulated genes) were identified in DLGG compared to NG...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28923001/a-molecular-view-of-the-normal-human-thyroid-structure-and-function-reconstructed-from-its-reference-transcriptome-map
#10
Lorenza Vitale, Allison Piovesan, Francesca Antonaros, Pierluigi Strippoli, Maria Chiara Pelleri, Maria Caracausi
BACKGROUND: The thyroid is the earliest endocrine structure to appear during human development, and thyroid hormones are necessary for proper organism development, in particular for the nervous system and heart, normal growth and skeletal maturation. To date a quantitative, validated transcriptional atlas of the whole normal human thyroid does not exist and the availability of a detailed expression map might be an excellent occasion to investigate the many features of the thyroid transcriptome...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28918100/transcriptomic-and-epigenomic-biomarkers-of-antidepressant-response
#11
REVIEW
Raoul Belzeaux, Rixing Lin, Chelsey Ju, Marc-Aurele Chay, Laura M Fiori, Pierre-Eric Lutz, Gustavo Turecki
BACKGROUND: Antidepressant treatment is associated with a high rate of poor response, and thus, biomarker development is warranted. METHODS: We aimed to synthesize studies investigating gene expression, small RNAs, and epigenomic biomarkers of antidepressant response. We conducted a narrative review of the literature. RESULTS: Firstly, we detailed the challenges involved, in terms of biological tissues, relevant study time frames, and mandatory statistical tools...
September 8, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28916533/sex-differences-in-the-prevalence-of-genetic-mutations-in-ftd-and-als-a-meta-analysis
#12
REVIEW
Ashley F Curtis, Mario Masellis, Ging-Yuek Robin Hsiung, Rahim Moineddin, Kathy Zhang, Bonnie Au, Geneva Millett, Ian Mackenzie, Ekaterina Rogaeva, Mary C Tierney
OBJECTIVE: To conduct a meta-analysis that investigates sex differences in the prevalence of mutations in the 3 most common genes that cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD)-chromosome 9 open reading frame 72 (C9orf72), progranulin (GRN), or microtubule-associated protein tau (MAPT)-in patients clinically diagnosed with these conditions. METHODS: MEDLINE, EMBASE, and PsycINFO databases were searched (inception to June 30, 2016)...
September 15, 2017: Neurology
https://www.readbyqxmd.com/read/28915673/prognositic-value-of-cd73-adenosinergic-pathway-in-solid-tumor-a-meta-analysis-and-systematic-review
#13
Rong Wang, Yingying Zhang, Xia Lin, Yalin Gao, Ying Zhu
CD73 is a glycosylphosphatidylinositol (GPI) anchored cell surface protein that is encoded by NT5E gene, plays multiple roles in tumor processes. Previous studies have presented a potential value of CD73 served as a detectable biomarker for prognosis of several solid tumors, but the results were more controversially. A comprehensive meta-analysis was conducted to precisely evaluate the prognostic role of CD73 in solid tumors. The included studies were searched in PubMed, Web of Science and EBSCO from Jan 1990 to Jan 2016...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28903437/meta-analysis-of-micrornas-expression-in-head-and-neck-cancer-uncovering-association-with-outcome-and-mechanisms
#14
Joshua Lubov, Mariana Maschietto, Iman Ibrahim, Alex Mlynarek, Michael Hier, Luiz Paulo Kowalski, Moulay A Alaoui-Jamali, Sabrina Daniela da Silva
Head and neck squamous cell carcinoma (HNSCC) is often diagnosed at advanced stages, incurring significant high mortality and morbidity. This review explored the risk stratification of miRNAs, and investigated the impact of miRNA networking in HNSCC prognostication. We performed a meta-analysis and a systematic literature search on online databases for papers published prior to December 1, 2016. The list of miRNAs was uploaded to MetacoreTM to construct a protein-protein interaction network, which was used to identify targets of the miRNAs and potential drugs...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28903366/systematic-analysis-of-coronary-artery-disease-datasets-revealed-the-potential-biomarker-and-treatment-target
#15
Yan Shi, Sijin Yang, Man Luo, Wei-Dong Zhang, Zun-Ping Ke
Coronary artery disease caused about 1 of every 7 deaths in the United States and early prevention was potential to decrease the incidence and mortality. We aimed to figure the genes involving in the coronary artery disease using meta-anlaysis. Five datasets of coronary heart disease from GEO series were retrieved and data preprocessing and quality control were carried out. Moderated t-test was used to decide the differentially expressed genes for a single dataset. And the combined p-value using systematic-analysis methods were conducted using MetaDE...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28902444/genomewide-association-studies-of-suicide-attempts-in-us-soldiers
#16
Murray B Stein, Erin B Ware, Colter Mitchell, Chia-Yen Chen, Susan Borja, Tianxi Cai, Catherine L Dempsey, Carol S Fullerton, Joel Gelernter, Steven G Heeringa, Sonia Jain, Ronald C Kessler, James A Naifeh, Matthew K Nock, Stephan Ripke, Xiaoying Sun, Jean C Beckham, Nathan A Kimbrel, Robert J Ursano, Jordan W Smoller
Suicide is a global public health problem with particular resonance for the US military. Genetic risk factors for suicidality are of interest as indicators of susceptibility and potential targets for intervention. We utilized population-based nonclinical cohorts of US military personnel (discovery: N = 473 cases and N = 9778 control subjects; replication: N = 135 cases and N = 6879 control subjects) and a clinical case-control sample of recent suicide attempters (N = 51 cases and N = 112 control subjects) to conduct GWAS of suicide attempts (SA)...
September 13, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28901446/a-support-vector-machine-classifier-for-the-prediction-of-osteosarcoma-metastasis-with-high-accuracy
#17
Yunfei He, Jun Ma, Xiaojian Ye
In this study, gene expression profiles of osteosarcoma (OS) were analyzed to identify critical genes associated with metastasis. Five gene expression datasets were screened and downloaded from Gene Expression Omnibus (GEO). Following assessment by MetaQC, the dataset GSE9508 was excluded for poor quality. Subsequently, differentially expressed genes (DEGs) between metastatic and non-metastatic OS were identified using meta‑analysis. A protein-protein interaction (PPI) network was constructed with information from Human Protein Reference Database (HPRD) for the DEGs...
September 7, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28899396/transcriptomic-meta-analysis-identifies-gene-expression-characteristics-in-various-samples-of-hiv-infected-patients-with-nonprogressive-disease
#18
Le-Le Zhang, Zi-Ning Zhang, Xian Wu, Yong-Jun Jiang, Ya-Jing Fu, Hong Shang
BACKGROUND: A small proportion of HIV-infected patients remain clinically and/or immunologically stable for years, including elite controllers (ECs) who have undetectable viremia (<50 copies/ml) and long-term nonprogressors (LTNPs) who maintain normal CD4(+) T cell counts for prolonged periods (>10 years). However, the mechanism of nonprogression needs to be further resolved. In this study, a transcriptome meta-analysis was performed on nonprogressor and progressor microarray data to identify differential transcriptome pathways and potential biomarkers...
September 12, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28892059/a-meta-analysis-of-genome-wide-association-studies-identifies-17-new-parkinson-s-disease-risk-loci
#19
Diana Chang, Mike A Nalls, Ingileif B Hallgrímsdóttir, Julie Hunkapiller, Marcel van der Brug, Fang Cai, Geoffrey A Kerchner, Gai Ayalon, Baris Bingol, Morgan Sheng, David Hinds, Timothy W Behrens, Andrew B Singleton, Tushar R Bhangale, Robert R Graham
Common variant genome-wide association studies (GWASs) have, to date, identified >24 risk loci for Parkinson's disease (PD). To discover additional loci, we carried out a GWAS comparing 6,476 PD cases with 302,042 controls, followed by a meta-analysis with a recent study of over 13,000 PD cases and 95,000 controls at 9,830 overlapping variants. We then tested 35 loci (P < 1 × 10(-6)) in a replication cohort of 5,851 cases and 5,866 controls. We identified 17 novel risk loci (P < 5 × 10(-8)) in a joint analysis of 26,035 cases and 403,190 controls...
September 11, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28881962/applying-meta-analysis-to-genotype-tissue-expression-data-from-multiple-tissues-to-identify-eqtls-and-increase-the-number-of-egenes
#20
Dat Duong, Lisa Gai, Sagi Snir, Eun Yong Kang, Buhm Han, Jae Hoon Sul, Eleazar Eskin
Motivation: There is recent interest in using gene expression data to contextualize findings from traditional genome-wide association studies (GWAS). Conditioned on a tissue, expression quantitative trait loci (eQTLs) are genetic variants associated with gene expression, and eGenes are genes whose expression levels are associated with genetic variants. eQTLs and eGenes provide great supporting evidence for GWAS hits and important insights into the regulatory pathways involved in many diseases...
July 15, 2017: Bioinformatics
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