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gene expression meta-analysis

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https://www.readbyqxmd.com/read/29328493/meta-analysis-of-mrna-expression-profiles-to-identify-differentially-expressed-genes-in-lung-adenocarcinoma-tissue-from-smokers-and-non-smokers
#1
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
https://www.readbyqxmd.com/read/29328363/support-vector-machine-classifier-for-prediction-of-the-metastasis-of-colorectal-cancer
#2
Jiajun Zhi, Jiwei Sun, Zhongchuan Wang, Wenjun Ding
Colorectal cancer (CRC) is one of the most common cancers and a major cause of mortality. The present study aimed to identify potential biomarkers for CRC metastasis and uncover the mechanisms underlying the etiology of the disease. The five datasets GSE68468, GSE62321, GSE22834, GSE14297 and GSE6988 were utilized in the study, all of which contained metastatic and non-metastatic CRC samples. Among them, three datasets were integrated via meta-analysis to identify the differentially expressed genes (DEGs) between the two types of samples...
January 2, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29326435/a-combined-analysis-of-genetically-correlated-traits-identifies-187-loci-and-a-role-for-neurogenesis-and-myelination-in-intelligence
#3
W D Hill, R E Marioni, O Maghzian, S J Ritchie, S P Hagenaars, A M McIntosh, C R Gale, G Davies, I J Deary
Intelligence, or general cognitive function, is phenotypically and genetically correlated with many traits, including a wide range of physical, and mental health variables. Education is strongly genetically correlated with intelligence (r g  = 0.70). We used these findings as foundations for our use of a novel approach-multi-trait analysis of genome-wide association studies (MTAG; Turley et al. 2017)-to combine two large genome-wide association studies (GWASs) of education and intelligence, increasing statistical power and resulting in the largest GWAS of intelligence yet reported...
January 11, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29322490/the-rs75932628-and-rs2234253-polymorphisms-of-the-trem2-gene-were-associated-with-susceptibility-to-frontotemporal-lobar-degeneration-in-caucasian-populations
#4
Wen-Hua Su, Zhi-Hong Shi, Shu-Ling Liu, Xiao-Dan Wang, Shuai Liu, Yong Ji
Polymorphisms of the triggering receptor expressed on myeloid cells 2 (TREM2) gene have been reported to be potentially associated with the risks of developing frontotemporal lobar degeneration (FTLD), with inconsistent conclusions. This study aims to comprehensively investigate the potential role of TREM2 variants in FTLD risks via a meta-analysis. We included a total of eight eligible articles. For TREM2 rs75932628, we observed a significantly increased FTLD risk in the models of T vs. C [Association Test, odds ratio (OR) = 2...
January 10, 2018: Annals of Human Genetics
https://www.readbyqxmd.com/read/29321020/meta-analysis-of-human-gene-expression-in-response-to-mycobacterium-tuberculosis-infection-reveals-potential-therapeutic-targets
#5
Zhang Wang, Seda Arat, Michal Magid-Slav, James R Brown
BACKGROUND: With the global emergence of multi-drug resistant strains of Mycobacterium tuberculosis, new strategies to treat tuberculosis are urgently needed such as therapeutics targeting potential human host factors. RESULTS: Here we performed a statistical meta-analysis of human gene expression in response to both latent and active pulmonary tuberculosis infections from nine published datasets. We found 1655 genes that were significantly differentially expressed during active tuberculosis infection...
January 10, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29313490/replication-study-transcriptional-amplification-in-tumor-cells-with-elevated-c-myc
#6
L Michelle Lewis, Meredith C Edwards, Zachary R Meyers, C Conover Talbot, Haiping Hao, David Blum, Elizabeth Iorns, Rachel Tsui, Alexandria Denis, Nicole Perfito, Timothy M Errington
As part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Blum et al., 2015), that described how we intended to replicate selected experiments from the paper 'Transcriptional amplification in tumor cells with elevated c-Myc' (Lin et al., 2012). Here we report the results. We found overexpression of c-Myc increased total levels of RNA in P493-6 Burkitt's lymphoma cells; however, while the effect was in the same direction as the original study (Figure 3E; Lin et al., 2012), statistical significance and the size of the effect varied between the original study and the two different lots of serum tested in this replication...
January 9, 2018: ELife
https://www.readbyqxmd.com/read/29311748/integrated-analysis-of-gene-expression-differences-in-twins-discordant-for-disease-and-binary-phenotypes
#7
Sivateja Tangirala, Chirag J Patel
While both genes and environment contribute to phenotype, deciphering environmental contributions to phenotype is a challenge. Furthermore, elucidating how different phenotypes may share similar environmental etiologies also is challenging. One way to identify environmental influences is through a discordant monozygotic (MZ) twin study design. Here, we assessed differential gene expression in MZ discordant twin pairs (affected vs. non-affected) for seven phenotypes, including chronic fatigue syndrome, obesity, ulcerative colitis, major depressive disorder, intermittent allergic rhinitis, physical activity, and intelligence quotient, comparing the spectrum of genes differentially expressed across seven phenotypes individually...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29306532/association-between-apical-periodontitis-and-interleukin-gene-polymorphisms-a-systematic-review-and-meta-analysis
#8
REVIEW
Alessandro G Salles, Lívia A A Antunes, Erika Calvano Küchler, Leonardo S Antunes
INTRODUCTION: Genetic polymorphisms may result in altered gene expression or functional changes of the encoded molecules and could possibly generate a deficient immunity. Consequently, individuals with specific genotypes could be more susceptible to disease or could present an increase in disease severity. Our study is aimed to verify, through a systematic review and meta-analysis registered in the PROSPERO database (CRD42016043905), whether currently available evidence supports a relationship between interleukin gene polymorphisms and apical periodontitis (AP)...
January 3, 2018: Journal of Endodontics
https://www.readbyqxmd.com/read/29303513/in-vitro-modeling-of-hepatocellular-carcinoma-molecular-subtypes-for-anti-cancer-drug-assessment
#9
Hadassa Hirschfield, C Billie Bian, Takaaki Higashi, Shigeki Nakagawa, Tizita Z Zeleke, Venugopalan D Nair, Bryan C Fuchs, Yujin Hoshida
Tractable experimental model that accounts for inter-tumor molecular heterogeneity is a key element of anti-cancer drug development. Hepatocellular carcinoma is known to exhibit highly heterogeneous molecular aberrations across the tumors, including somatic genetic and epigenetic alterations. Previous studies showed that molecular tumor subtypes determined by transcriptome, as a comprehensive functional readout, are reproducibly observed across global patient populations irrespective of geographic and etiological variations...
January 5, 2018: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29300726/regulation-of-circadian-clock-transcriptional-output-by-clock-bmal1
#10
Alexandra J Trott, Jerome S Menet
The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of 15% of the transcriptome and control the daily regulation of biological functions. The recent characterization of CLOCK:BMAL1 cistrome revealed that although CLOCK:BMAL1 binds synchronously to all of its target genes, its transcriptional output is highly heterogeneous. By performing a meta-analysis of several independent genome-wide datasets, we found that the binding of other transcription factors at CLOCK:BMAL1 enhancers likely contribute to the heterogeneity of CLOCK:BMAL1 transcriptional output...
January 4, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29297276/ale-automated-label-extraction-from-geo-metadata
#11
Cory B Giles, Chase A Brown, Michael Ripperger, Zane Dennis, Xiavan Roopnarinesingh, Hunter Porter, Aleksandra Perz, Jonathan D Wren
BACKGROUND: NCBI's Gene Expression Omnibus (GEO) is a rich community resource containing millions of gene expression experiments from human, mouse, rat, and other model organisms. However, information about each experiment (metadata) is in the format of an open-ended, non-standardized textual description provided by the depositor. Thus, classification of experiments for meta-analysis by factors such as gender, age of the sample donor, and tissue of origin is not feasible without assigning labels to the experiments...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29291240/meta-analysis-of-micrornas-dysregulated-in-the-hippocampal-dentate-gyrus-of-animal-models-of-epilepsy
#12
Prashant K Srivastava, Paolo Roncon, Katarzyna Lukasiuk, Jan A Gorter, Eleonora Aronica, Asla Pitkänen, Enrico Petretto, Michael R Johnson, Michele Simonato
The identification of mechanisms transforming normal to seizure-generating tissue after brain injury is key to developing new antiepileptogenic treatments. MicroRNAs (miRNAs) may act as regulators and potential treatment targets for epileptogenesis. Here, we undertook a meta-analysis of changes in miRNA expression in the hippocampal dentate gyrus (DG) following an epileptogenic insult in three epilepsy models. We identified 26 miRNAs significantly differentially expressed during epileptogenesis, and five differentially expressed in chronic epilepsy...
November 2017: ENeuro
https://www.readbyqxmd.com/read/29288038/brg1-is-correlated-with-poor-prognosis-in-colorectal-cancer
#13
Jung-Soo Pyo, Byoung Kwan Son, Dongwook Oh, Eun Kyung Kim
Brahma-related gene 1 (BRG1), a component of the chromatin-remodeling complex, regulates transcription by remodeling the chromatin structure. The present study aimed to elucidate the clinicopathological significance and prognostic role of BRG1 in colorectal cancer (CRC). We investigated the correlation between BRG1 expression and clinicopathological parameters, including prognosis, using immunohistochemistry on 266 archival paraffin-embedded CRC tissues. In addition, to confirm the prognostic role of BRG1 in malignant tumors, we performed a meta-analysis of nine eligible studies and the current study...
December 26, 2017: Human Pathology
https://www.readbyqxmd.com/read/29286420/comprehensive-workflow-for-the-genome-wide-identification-and-expression-meta-analysis-of-the-atl-e3-ubiquitin-ligase-gene-family-in-grapevine
#14
Pietro Ariani, Elodie Vandelle, Darren Wong, Alejandro Giorgetti, Andrea Porceddu, Salvatore Camiolo, Annalisa Polverari
Classification and nomenclature of genes in a family can significantly contribute to the description of the diversity of encoded proteins and to the prediction of family functions based on several features, such as the presence of sequence motifs or of particular sites for post-translational modification and the expression profile of family members in different conditions. This work describes a detailed protocol for gene family characterization. Here, the procedure is applied to the characterization of the Arabidopsis Tóxicos in Levadura (ATL) E3 ubiquitin ligase family in grapevine...
December 22, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29286069/a-16-gene-expression-signature-to-distinguish-stage%C3%A2-i-from-stage%C3%A2-ii-lung-squamous-carcinoma
#15
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
https://www.readbyqxmd.com/read/29285225/the-protective-value-of-mir-204-5p-for-prognosis-and-its-potential-gene-network-in-various-malignancies-a-comprehensive-exploration-based-on-rna-seq-high-throughput-data-and-bioinformatics
#16
Zhi-Hua Ye, Dong-Yue Wen, Xiao-Yong Cai, Liang Liang, Pei-Rong Wu, Hui Qin, Hong Yang, Yun He, Gang Chen
Purpose: The prognostic role of miR-204-5p (previous ID: miR-204) is varied and inconclusive in diverse types of malignant neoplasm. Therefore, the purposes of the study comprehensively explore the overall prognostic role of miR-204-5p based on high-throughput microRNA sequencing data, and to investigate the potential role of miR-204-5p via bioinformatics approaches. Materials and Methods: The data of microRNA sequencing and survival were downloaded from The Cancer Genome Atlas (TCGA), and the prognostic value of miR-204-5p was analyzed by using Kaplan-Meier and univariate cox regressions...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29285217/identification-of-novel-gene-expression-signature-in-lung-adenocarcinoma-by-using-next-generation-sequencing-data-and-bioinformatics-analysis
#17
Ya-Ling Hsu, Jen-Yu Hung, Yen-Lung Lee, Feng-Wei Chen, Kuo-Feng Chang, Wei-An Chang, Ying-Ming Tsai, Inn-Wen Chong, Po-Lin Kuo
Lung adenocarcinoma is one of the leading causes of cancer-related death worldwide. We showed transcriptomic profiles in three pairs of tumors and adjacent non-tumor lung tissues using next-generation sequencing (NGS) to screen protein-coding RNAs and microRNAs. Combined with meta-analysis from the Oncomine and Gene Expression Omnibus (GEO) databases, we identified a representative genetic expression signature in lung adenocarcinoma. There were 9 upregulated genes, and 8 downregulated genes in lung adenocarcinoma...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29280245/systematic-genetic-analyses-of-genome-wide-association-study-data-reveal-an-association-between-the-key-nucleosome-remodeling-and-deacetylase-complex-and-bipolar-disorder-development
#18
Bo Xiang, Kezhi Liu, Minglan Yu, Xuemei Liang, Jin Zhang, Wei Lei, Chaohua Huang, Jing Chen, Xiaochu Gu, Nian Li, Guoying Wu, Yan Wang, Wenying He, Jinhua Tan, Tao Zhang
BACKGROUND: Genome-wide association studies (GWASs) are used to identify genetic variants for association with bipolar disorder (BD) risk; however, each GWAS can only reveal a small fraction of this association. This study systematically analyzed multiple GWAS data sets to provide further insights into potential causal BD processes by integrating the results of Psychiatric Genomics Consortium Phase I (PGC-I) for BD with core human pathways and functional networks. METHODS: The i-Gsea4GwasV2 program was used to analyze data from the PGC-I GWAS for BD (the pathways came from Reactome), as well as the nominally significant pathways...
December 27, 2017: Bipolar Disorders
https://www.readbyqxmd.com/read/29278884/decreased-expression-of-pth1r-is-a-poor-prognosis-in-hepatocellular-carcinoma
#19
Hui-Ju Wang, Liang Wang, Shu-Shu Song, Xiang-Lei He, Hong-Ying Pan, Zhi-Ming Hu, Xiao-Zhou Mou
BACKGROUND AND AIM: Hypercalcemia is a potentially fatal and not rare complication of hepatocellular carcinoma (HCC), and its underlying mechanism remains unclear. Parathyroid hormone (PTH) is the most important regulator of the concentrations of calcium and phosphate in blood; parathyroid hormone-related protein (PTHrP) was the most frequent cause of humoral hypercalcemia of malignancy; parathyroid hormone 1 receptor (PTH1R) is the common receptor for PTH and PTHrP. The aim of this study is to investigate the expression of PTH, PTHrP, and PTH1R in HCC tissues, and their relationship with clinical pathological characters in HCC...
December 15, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/29274975/association-analysis-for-udder-index-and-milking-speed-with-imputed-whole-genome-sequence-variants-in-nordic-holstein-cattle
#20
Júlia Gazzoni Jardim, Bernt Guldbrandtsen, Mogens Sandø Lund, Goutam Sahana
Genome-wide association testing facilitates the identification of genetic variants associated with complex traits. Mapping genes that promote genetic resistance to mastitis could reduce the cost of antibiotic use and enhance animal welfare and milk production by improving outcomes of breeding for udder health. Using imputed whole-genome sequence variants, we carried out association studies for 2 traits related to udder health, udder index, and milking speed in Nordic Holstein cattle. A total of 4,921 bulls genotyped with the BovineSNP50 BeadChip array were imputed to high-density genotypes (Illumina BovineHD BeadChip, Illumina, San Diego, CA) and, subsequently, to whole-genome sequence variants...
December 20, 2017: Journal of Dairy Science
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