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gene expression meta analysis

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https://www.readbyqxmd.com/read/28821015/extracting-replicable-associations-across-multiple-studies-empirical-bayes-algorithms-for-controlling-the-false-discovery-rate
#1
David Amar, Ron Shamir, Daniel Yekutieli
In almost every field in genomics, large-scale biomedical datasets are used to report associations. Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we propose a new method to allow joint analysis of multiple studies. Given a set of p-values obtained from each study, the goal is to identify associations that recur in at least k > 1 studies while controlling the false discovery rate. We propose several new algorithms that differ in how the study dependencies are modeled, and compare them and extant methods under various simulated scenarios...
August 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28818099/biosemantics-guided-gene-expression-profiling-of-sj%C3%A3-gren-s-syndrome-a-comparative-analysis-with-systemic-lupus-erythematosus-and-rheumatoid-arthritis
#2
Nirav R Shah, Braxton D Noll, Craig B Stevens, Michael T Brennan, Farah B Mougeot, Jean-Luc C Mougeot
BACKGROUND: Sjögren's syndrome (SS) shares many clinical and pathological similarities with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). These autoimmune diseases mostly affect women. In this study, concept profile analysis (CPA) and gene expression meta-analysis were used to identify genes potentially involved in SS pathogenesis. METHODS: Human genes associated with SS, SLE, and RA were identified using the CPA tool, Anni 2.1. The differential mRNA expression of genes common to SS and SLE (SS-SLE) was determined in female peripheral blood mononuclear cells (PBMCs) using NCBI-GEO2R...
August 17, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28813680/antibiotics-disrupt-coordination-between-transcriptional-and-phenotypic-stress-responses-in-pathogenic-bacteria
#3
Paul A Jensen, Zeyu Zhu, Tim van Opijnen
Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28803142/identification-and-characterization-of-a-long-non-coding-rna-up-regulated-during-hiv-1-infection
#4
Thomas S Postler, Shara N Pantry, Ronald C Desrosiers, Sankar Ghosh
Long non-coding RNAs (lncRNAs) are rapidly emerging as important regulators of a diverse array of cellular functions. Here, we describe a meta-analysis of two independent RNA-seq studies to identify lncRNAs that are differentially expressed upon HIV-1 infection. Only three lncRNA genes exhibited altered expression of ≥ 2-fold in HIV-1-infected cells. Of these, the uncharacterized lncRNA LINC00173 was chosen for further study. Both transcript variants of LINC00173 (lnc173 TSV1 and 2) could be detected by qPCR, localized predominantly to the nucleus and were reproducibly up-regulated during infection...
August 10, 2017: Virology
https://www.readbyqxmd.com/read/28801378/relationship-between-mir-146a-rs2910164-g-c-polymorphism-and-digestive-system-cancer-susceptibility-a-meta-analysis
#5
Xin Xiong, Junfeng Yan, Linghua Li, Yun Li, Yi Cao, Yi Tu, Jinhong Mei
MicroRNAs (miRNAs) are identified negatively regulating gene expression and acting as oncogenes or tumor suppressors in tumorigenesis. The association between miR-146a rs2910164 (G>C) polymorphism and susceptibility to digestive system cancers was contradictory and inconsistent in previously published studies. Presently, we performed a comprehensive literature retrieve on PubMed, Web of Science, Embase, Wanfang and CNKI databases to identify all relevant studies published before July 30, 2016. Odds ratio (OR) and 95% confidential interval (95%CI) were used to calculate the relationship between miR-146a rs2910164 (G>C) polymorphism and digestive system cancers susceptibility...
August 2017: Annals of Clinical and Laboratory Science
https://www.readbyqxmd.com/read/28796378/functional-genetic-variants-of-xrcc4-and-ercc1-predict-survival-of-gastric-cancer-patients-treated-with-chemotherapy-by-regulating-the-gene-expression
#6
Lei Cheng, Lixin Qiu, Mengyun Wang, Ruoxin Zhang, Menghong Sun, Xiaodong Zhu, Yanong Wang, Qingyi Wei
DNA repair protects genomic integrity and may modulate chemotherapy efficacy. Few large-scale studies have evaluated predictive roles of genetic variants of DNA repair genes in survival of Chinese gastric cancer (GCa) patients treated with chemotherapy. Here, we assessed the roles of 35 single nucleotide polymorphisms (SNPs) in DNA repair genes in survival of 1,002 GCa patients, of whom 694 received chemotherapy and 308 did not. Among patients receiving chemotherapy, the ERCC1 rs2298881A allele was associated with a better survival [hazards ratio (HR) =0...
August 10, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28794909/role-of-the-lf-sine-derived-distal-isl1-enhancer-in-patients-with-classic-bladder-exstrophy
#7
Rong Zhang, Michael Knapp, Franziska Kause, Heiko Reutter, Michael Ludwig
A genome-wide association study and meta-analysis identified ISL1 as the first genome-wide significant susceptibility gene for classic bladder exstrophy (CBE). A short interspersed repetitive element (SINE), first detected in lobe-finned fishes (LF-SINE), was shown to drive Isl1 expression in embryonic mouse genital eminence. Hence, we assumed this enhancer a conclusive target for mutations associated with CBE formation and analyzed a cohort of 200 CBE patients. Although we identified two enhancer variants in five CBE patients, their clinical significance seems unlikely, implying that sequence variants in the ISL1 LF-SINE enhancer are not frequently associated with CBE...
September 2017: Journal of Pediatric Genetics
https://www.readbyqxmd.com/read/28794466/a-family-of-archaea-like-carboxylesterases-preferentially-expressed-in-the-symbiotic-phase-of-the-mychorrizal-fungus-tuber-melanosporum
#8
Davide Cavazzini, Guido Grossi, Elisabetta Levati, Francesca Vallese, Barbara Montanini, Angelo Bolchi, Giuseppe Zanotti, Simone Ottonello
An increasing number of esterases is being revealed by (meta) genomic sequencing projects, but few of them are functionally/structurally characterized, especially enzymes of fungal origin. Starting from a three-member gene family of secreted putative "lipases/esterases" preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum ("black truffle"), we show here that these enzymes (TmelEST1-3) are dimeric, heat-resistant carboxylesterases capable of hydrolyzing various short/medium chain p-nitrophenyl esters...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28794112/fifteen-genetic-loci-associated-with-the-electrocardiographic-p-wave
#9
Ingrid E Christophersen, Jared W Magnani, Xiaoyan Yin, John Barnard, Lu-Chen Weng, Dan E Arking, Maartje N Niemeijer, Steven A Lubitz, Christy L Avery, Qing Duan, Stephan B Felix, Joshua C Bis, Kathleen F Kerr, Aaron Isaacs, Martina Müller-Nurasyid, Christian Müller, Kari E North, Alex P Reiner, Lesley F Tinker, Jan A Kors, Alexander Teumer, Astrid Petersmann, Moritz F Sinner, Petra Buzkova, Jonathan D Smith, David R Van Wagoner, Uwe Völker, Melanie Waldenberger, Annette Peters, Thomas Meitinger, Marian C Limacher, Kirk C Wilhelmsen, Bruce M Psaty, Albert Hofman, Andre Uitterlinden, Bouwe P Krijthe, Zhu-Ming Zhang, Renate B Schnabel, Stefan Kääb, Cornelia van Duijn, Jerome I Rotter, Nona Sotoodehnia, Marcus Dörr, Yun Li, Mina K Chung, Elsayed Z Soliman, Alvaro Alonso, Eric A Whitsel, Bruno H Stricker, Emelia J Benjamin, Susan R Heckbert, Patrick T Ellinor
BACKGROUND: The P wave on an ECG is a measure of atrial electric function, and its characteristics may serve as predictors for atrial arrhythmias. Increased mean P-wave duration and P-wave terminal force traditionally have been used as markers for left atrial enlargement, and both have been associated with increased risk of atrial fibrillation. Here, we explore the genetic basis of P-wave morphology through meta-analysis of genome-wide association study results for P-wave duration and P-wave terminal force from 12 cohort studies...
August 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28793203/rna-extraction-from-decaying-wood-for-meta-transcriptomic-analyses
#10
Martino Adamo, Samuele Voyron, Mariangela Girlanda, Roland Marmeisse
Wood decomposition is a key step of the terrestrial carbon cycle and of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating to wood decay we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds. This protocol was implemented on 22 wood samples representing as many tree species from 11 plant families in the Angiosperms and Gymnosperms...
August 9, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28790856/role-of-downregulated-mir-133a-3p-expression-in-bladder-cancer-a-bioinformatics-study
#11
Li Gao, Sheng-Hua Li, Yi-Xin Tian, Qing-Qing Zhu, Gang Chen, Yu-Yan Pang, Xiao-Hua Hu
It has been discovered that miR-133a-3p acts as a tumor suppressor in bladder cancer (BC). Nevertheless, the function of miR-133a-3p in BC remains unclarified. Thus, we carried out this study to validate the expression of miR-133a-3p in BC and provide insights into the molecular mechanism underlying it. To assess the expression of miR-133a-3p in BC, we searched eligible studies from literature and Gene expression Omnibus (GEO) to perform a meta-analysis. We also plotted the summary receiver operating characteristic (SROC) curve to evaluate the diagnostic ability of miR-133a-3p in BC...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28790842/association-of-fhit-expression-and-fhit-gene-hypermethylation-with-liver-cancer-risk-a-prisma-compliant-meta-analysis
#12
Yaping Zhang, Xiao Xu, Zhiliang Chen, Zhenhua Zhao
BACKGROUND: There have been suggestions that fragile histidine triad protein (FHIT) expression and FHIT gene hypermethylation were crucial to the pathogenesis of liver cancer. However, the conclusions remained unclear because of small sample size, disease subtype, and different detection techniques. Therefore, we performed a meta-analysis to estimate the associations of FHIT expression and FHIT gene hypermethylation with liver cancer pathogenesis. METHODS: Studies that were published in electronic databases, such as PubMed, Web of Knowledge, China National Knowledge Infrastructure (CNKI), VIP, and WanFang, were retrieved and selected for the meta-analysis...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28782484/gene-expression-meta-analysis-of-potential-metastatic-breast-cancer-markers
#13
R Bell, R Barraclough, O Vasieva
Breast cancer metastasis is a highly prevalent cause of death for European females. DNA microarray analysis has established that primary tumors, which remain localized, differ in gene expression from those that metastasize. The aim of the project was to validate suggested prognostic and therapeutic markers using meta-analysis of data on gene expression in metastatic and primary breast cancer tumors combined from 12 studies available from the Genevestigator database. Our analysis suggested that transcriptional expression of the COX2 gene is significantly downregulated in metastatic tissue compared to normal breast tissue, but is not downregulated in primary tumors compared with normal breast tissue and may be used as a differential marker in metastatic breast cancer diagnostics...
August 7, 2017: Current Molecular Medicine
https://www.readbyqxmd.com/read/28767431/correlation-between-protein-kinase-catalytic-subunit-alpha-1-gene-rs13361707-polymorphism-and-gastric-cancer-susceptibility-in-asian-populations
#14
Jianfeng Ni, Nan Shen, Jilei Tang, Kewei Ren
A single nucleotide polymorphism (SNP) of the protein kinase catalytic subunit alpha-1 gene (PRKAA1) that confers susceptibility to gastric cancer (GC) was identified by genome-wide association in several case-control studies. However, the results remained controversial and ambiguous. Therefore, we performed a larger meta-analysis to confirm this association. We searched the PubMed, Embase, WanFang, and CNKI databases, without any restriction on language, covering all papers published until Feb 22, 2017. Overall, 14 case-control studies with 14,485 cases and 14,792 controls were retrieved based on the search criteria...
July 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28767422/a-meta-analysis-of-transcriptomic-characterization-revealed-extracellular-matrix-pathway-involved-in-the-h5n1-and-h7n9-infections
#15
Feng Wen, Jinyue Guo, Guangzhi Tong, Dingren Bi, Qi Wang, Xiaomin Liu, Shuaiyong Wang, Tonglin Shan, Wu Tong, Yanjun Zhou, Guoxin Li, Hai Yu
Avian-origin H5N1 and H7N9 influenza A viruses are capable of causing lethal infection in humans, with serious lung pathology and leading to acute respiratory distress syndrome. The contribution of host response associated with the poor prognosis of H5N1 and H7N9 infections remains unclear. The aim of this study was to identify the host factors involved in the high pathogenicity of H5N1 and H7N9 by a systematical meta-analysis. The RNA-seq datasets related to H5N1, H7N9, and H1N1 infections with time series were retrieved from GEO...
July 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28767398/the-30-kb-deletion-in-the-apobec3-cluster-decreases-apobec3a-and-apobec3b-expression-and-creates-a-transcriptionally-active-hybrid-gene-but-does-not-associate-with-breast-cancer-in-the-european-population
#16
Katarzyna Klonowska, Wojciech Kluzniak, Bogna Rusak, Anna Jakubowska, Magdalena Ratajska, Natalia Krawczynska, Danuta Vasilevska, Karol Czubak, Marzena Wojciechowska, Cezary Cybulski, Jan Lubinski, Piotr Kozlowski
APOBEC3B, in addition to other members of the APOBEC3 gene family, has recently been intensively studied due to its identification as a gene whose activation in cancer is responsible for a specific pattern of massively occurring somatic mutations. It was recently shown that a common large deletion in the APOBEC3 cluster (the APOBEC3B deletion) may increase the risk of breast cancer. However, conflicting evidence regarding this association was also reported. In the first step of our study, using different approaches, including an in-house designed multiplex ligation-dependent probe amplification assay, we analyzed the structure of the deletion and showed that although the breakpoints are located in highly homologous regions, which may generate recurrent occurrence of similar but not identical deletions, there is no sign of deletion heterogeneity...
July 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28761826/the-inhibitory-effect-of-ginger-extract-on-ovarian-cancer-cell-line-application-of-systems-biology
#17
Roghiyeh Pashaei-Asl, Fatima Pashaei-Asl, Parvin Mostafa Gharabaghi, Khodadad Khodadadi, Mansour Ebrahimi, Esmaeil Ebrahimie, Maryam Pashaiasl
Purpose: Ginger is a natural compound with anti-cancer properties. The effects of ginger and its mechanism on ovarian cancer and its cell line model, SKOV-3, are unclear. In this study, we have evaluated the effect of ginger extract on SKOV-3. Methods: SKOV-3 cells were incubated with ginger extract for 24, 48 and 72 hours. Cell toxicity assay was performed. Different data mining algorithms were applied to highlight the most important features contributing to ginger inhibition on the SKOV-3 cell proliferation...
June 2017: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28754837/p53-independent-dux4-pathology
#18
Darko Bosnakovski, Micah D Gearhart, Erik A Toso, Olivia O Recht, Anja Cucak, Abhinav K Jain, Michelle C Barton, Michael Kyba
FSHD is a genetically dominant myopathy caused by mutations that disrupt repression of the normally silent DUX4 gene, which encodes a transcription factor that has been shown to interfere with myogenesis when misexpressed at very low levels in myoblasts, and to cause cell death when overexpressed at high levels. A previous report using adeno-associated virus to deliver high levels of DUX4 to mouse skeletal muscle demonstrated severe pathology that was suppressed on a p53 knockout background, implying that DUX4 acted through the p53 pathway...
July 28, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28746200/promising-significance-of-the-association-of-mir-204-5p-expression-with-clinicopathological-features-of-hepatocellular-carcinoma
#19
Yi-Huan Luo, Wei Tang, Xin Zhang, Zhong Tan, Wen-Liang Guo, Na Zhao, Si-Min Pang, Yi-Wu Dang, Min-Hua Rong, Ji Cao
Decreased level of miR-204-5p has been documented in various malignancies. However, the expression and clinical significance of miR-204-5p in hepatocellular carcinoma has not been investigated. The aim of this study is to examine the relationship between miR-204-5p expression and clinicopathological features in hepatocellular carcinoma (HCC) as well as to predict the relevant signaling pathways. The miR-204-5p expression level was detected in HCC and in matched paraneoplastic liver from 95 formalin-fixed paraffin-embedded tissues by the real-time reverse transcription polymerized chain reaction (qRT-PCR)...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28744145/a-comprehensive-insight-into-the-clinicopathologic-significance-of-mir-144-3p-in-hepatocellular-carcinoma
#20
Hai-Wei Liang, Zhi-Hua Ye, Shu-Ya Yin, Wei-Jia Mo, Han-Lin Wang, Jin-Che Zhao, Guo-Mei Liang, Zhen-Bo Feng, Gang Chen, Dian-Zhong Luo
BACKGROUND: Studies which focused on the character of miR-144-3p in hepatocellular carcinoma (HCC) are limited. This study aimed to explore the expression, clinical significance and the potential targets of miR-144-3p in HCC. METHODS: The Cancer Genome Atlas (TCGA) and a cohort of 95 cases of HCC were applied to investigate aberrant miR-144-3p expression in HCC. A meta-analysis was performed to accumulate data on miR-144-3p expression in HCC based on TCGA, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and Gene Expression Omnibus (GEO)...
2017: OncoTargets and Therapy
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