keyword
MENU ▼
Read by QxMD icon Read
search

gene expression meta analysis

keyword
https://www.readbyqxmd.com/read/28213955/the-skin-barrier-function-gene-spink5-is-associated-with-challenge-proven-ige-mediated-food-allergy-in-infants
#1
Sarah E Ashley, Hern-Tze Tina Tan, Peter Vuillermin, Shyamali C Dharmage, Mimi L K Tang, Jennifer Koplin, Lyle C Gurrin, Adrian Lowe, Caroline Lodge, Anne-Louise Ponsonby, John Molloy, Pamela Martin, Melanie C Matheson, Richard Saffery, Katrina J Allen, Justine A Ellis, David Martino
BACKGROUND: A defective skin barrier is hypothesised to be an important route of sensitisation to dietary antigens, and may lead to food allergy in some children. Missense mutations in the Serine peptidase inhibitor kazal type 5 (SPINK5) skin barrier gene have previously been associated with allergic conditions. OBJECTIVE: To determine whether genetic variants in and around SPINK5 are associated with IgE mediated food allergy. METHOD: We genotyped 71 'tag' single nucleotide polymorphisms (tag-SNPs) within a region spanning ~263 kilobases (kb) including SPINK5 (~61kb) in n=722 (n=367 food allergic, n=199 food sensitised, tolerant and n=156 non-food allergic controls) 12-month infants (discovery sample) phenotyped for food allergy with the gold standard oral food challenge (OFC)...
February 18, 2017: Allergy
https://www.readbyqxmd.com/read/28212542/two-stage-genome-wide-association-study-identifies-a-novel-susceptibility-locus-associated-with-melanoma
#2
Katherine J Ransohoff, Wenting Wu, Hyunje G Cho, Harvind C Chahal, Yuan Lin, Hong-Ji Dai, Christopher I Amos, Jeffrey E Lee, Jean Y Tang, David A Hinds, Jiali Han, Qingyi Wei, Kavita Y Sarin
Genome-wide association studies have identified 21 susceptibility loci associated with melanoma. These loci implicate genes affecting pigmentation, nevus count, telomere maintenance, and DNA repair in melanoma risk. Here, we report the results of a two-stage genome-wide association study of melanoma. The stage 1 discovery phase consisted of 4,842 self-reported melanoma cases and 286,565 controls of European ancestry from the 23andMe research cohort and the stage 2 replication phase consisted of 1,804 melanoma cases and 1,026 controls from the University of Texas M...
February 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28210261/a-comprehensive-gene-expression-meta-analysis-identifies-novel-immune-signatures-in-rheumatoid-arthritis-patients
#3
Sumbul Afroz, Jeevan Giddaluru, Sandeep Vishwakarma, Saima Naz, Aleem Ahmed Khan, Nooruddin Khan
Rheumatoid arthritis (RA), a symmetric polyarticular arthritis, has long been feared as one of the most disabling forms of arthritis. Identification of gene signatures associated with RA onset and progression would lead toward development of novel diagnostics and therapeutic interventions. This study was undertaken to identify unique gene signatures of RA patients through large-scale meta-profiling of a diverse collection of gene expression data sets. We carried out a meta-analysis of 8 publicly available RA patients' (107 RA patients and 76 healthy controls) gene expression data sets and further validated a few meta-signatures in RA patients through quantitative real-time PCR (RT-qPCR)...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28207831/the-relationship-between-rassf1a-gene-promoter-methylation-and-the-susceptibility-and-prognosis-of-melanoma-a-meta-analysis-and-bioinformatics
#4
Chihao Shao, Wenzhu Dai, Haili Li, Wenru Tang, Shuting Jia, Xiaoming Wu, Ying Luo
BACKGROUND: The function of the tumor suppressor gene RASSF1A in cancer cells has been detailed in many studies. However, due to the methylation of its promoter, the expression of RASSF1A is missing in most cancers. In the literature, we found that the conclusion regarding the relationship between RASSF1A gene promoter methylation and the susceptibility and prognosis of melanoma was not unified. This study adopts the use of a meta-analysis and bioinformatics to explore the relationship between RASSF1A gene promoter methylation and the susceptibility and prognosis of melanoma...
2017: PloS One
https://www.readbyqxmd.com/read/28203683/identification-of-unique-venous-thromboembolism-susceptibility-variants-in-african-americans
#5
John A Heit, Sebastian M Armasu, Bryan M McCauley, Iftikhar J Kullo, Hugues Sicotte, Jyotishman Pathak, Christopher G Chute, Omri Gottesman, Erwin P Bottinger, Joshua C Denny, Dan M Roden, Rongling Li, Marylyn D Ritchie, Mariza de Andrade
To identify novel single nucleotide polymorphisms (SNPs) associated with venous thromboembolism (VTE) in African-Americans (AAs), we performed a genome-wide association study (GWAS) of VTE in AAs using the Electronic Medical Records and Genomics (eMERGE) Network, comprised of seven sites each with DNA biobanks (total ~39,200 unique DNA samples) with genome-wide SNP data (imputed to 1000 Genomes Project cosmopolitan reference panel) and linked to electronic health records (EHRs). Using a validated EHR-driven phenotype extraction algorithm, we identified VTE cases and controls and tested for an association between each SNP and VTE using unconditional logistic regression, adjusted for age, sex, stroke, site-platform combination and sickle cell risk genotype...
February 16, 2017: Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/28199355/transcriptomic-meta-analysis-reveals-up-regulation-of-gene-expression-functional-in-osteoclast-differentiation-in-human-septic-shock
#6
Samanwoy Mukhopadhyay, Pravat K Thatoi, Abhay D Pandey, Bidyut K Das, Balachandran Ravindran, Samsiddhi Bhattacharjee, Saroj K Mohapatra
Septic shock is a major medical problem with high morbidity and mortality and incompletely understood biology. Integration of multiple data sets into a single analysis framework empowers discovery of new knowledge about the condition that may have been missed by individual analysis of each of these datasets. Electronic search was performed on medical literature and gene expression databases for selection of transcriptomic studies done in circulating leukocytes from human subjects suffering from septic shock...
2017: PloS One
https://www.readbyqxmd.com/read/28199342/meta-qtl-for-resistance-to-white-mold-in-common-bean
#7
Renato C C Vasconcellos, O Blessing Oraguzie, Alvaro Soler, Haidar Arkwazee, James R Myers, Juan J Ferreira, Qijian Song, Phil McClean, Phillip N Miklas
White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease that limits common bean production and quality worldwide. The host-pathogen interaction is complex, with partial resistance in the host inherited as a quantitative trait with low to moderate heritability. Our objective was to identify meta-QTL conditioning partial resistance to white mold from individual QTL identified across multiple populations and environments. The physical positions for 37 individual QTL were identified across 14 recombinant inbred bi-parental populations (six new, three re-genotyped, and five from the literature)...
2017: PloS One
https://www.readbyqxmd.com/read/28187435/glucose-transporter-glut1-expression-and-clinical-outcome-in-solid-tumors-a-systematic-review-and-meta-analysis
#8
Ji Wang, Chenyang Ye, Cong Chen, Hanchu Xiong, Binbin Xie, Jichun Zhou, Yongxia Chen, Shu Zheng, Linbo Wang
Glucose transporter 1 (GLUT1), the uniporter protein encoded by the SLC2A1 gene, is a key rate-limiting factor in the transport of glucose in cancer cells, and frequently expressed in a significant proportion of human cancers. Numerous studies have reported paradoxical evidence of the relationship between GLUT1 expression and prognosis in solid human tumors. To address this discrepancy, we conducted a thorough search of Pubmed and Web of Science for studies evaluating the expression of GLUT1 and overall survival (OS) and disease-free survival (DFS) in patients with solid cancer from 1993 to April 2016...
February 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28184370/metaproteomics-as-a-complementary-approach-to-gut-microbiota-in-health-and-disease
#9
REVIEW
Bernardo A Petriz, Octávio L Franco
Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28183295/meta-analysis-of-gene-expression-in-relapsed-childhood-b-acute-lymphoblastic-leukemia
#10
Yock-Ping Chow, Hamidah Alias, Rahman Jamal
BACKGROUND: Relapsed pediatric B-acute lymphoblastic leukemia (B-ALL) remains as the leading cause of cancer death among children. Other than stem cell transplantation and intensified chemotherapy, no other improved treatment strategies have been approved clinically. Gene expression profiling represents a powerful approach to identify potential biomarkers and new therapeutic targets for various diseases including leukemias. However, inadequate sample size in many individual experiments has failed to provide adequate study power to yield translatable findings...
February 10, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28176844/isl1-is-a-major-susceptibility-gene-for-classic-bladder-exstrophy-and-a-regulator-of-urinary-tract-development
#11
Rong Zhang, Michael Knapp, Kentaro Suzuki, Daiki Kajioka, Johanna M Schmidt, Jonas Winkler, Öznur Yilmaz, Michael Pleschka, Jia Cao, Christina Clementson Kockum, Gillian Barker, Gundela Holmdahl, Glenda Beaman, David Keene, Adrian S Woolf, Raimondo M Cervellione, Wei Cheng, Simon Wilkins, John P Gearhart, Fabio Sirchia, Massimo Di Grazia, Anne-Karolin Ebert, Wolfgang Rösch, Jörg Ellinger, Ekkehart Jenetzky, Nadine Zwink, Wout F Feitz, Carlo Marcelis, Johannes Schumacher, Federico Martinón-Torres, Martin Lloyd Hibberd, Chiea Chuen Khor, Stefanie Heilmann-Heimbach, Sandra Barth, Simeon A Boyadjiev, Alfredo Brusco, Michael Ludwig, William Newman, Agneta Nordenskjöld, Gen Yamada, Benjamin Odermatt, Heiko Reutter
Previously genome-wide association methods in patients with classic bladder exstrophy (CBE) found association with ISL1, a master control gene expressed in pericloacal mesenchyme. This study sought to further explore the genetics in a larger set of patients following-up on the most promising genomic regions previously reported. Genotypes of 12 markers obtained from 268 CBE patients of Australian, British, German Italian, Spanish and Swedish origin and 1,354 ethnically matched controls and from 92 CBE case-parent trios from North America were analysed...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28168095/identification-of-four-potential-predicting-mirna-biomarkers-for-multiple-myeloma-from-published-datasets
#12
Tian Xiang, Ai-Xin Hu, Peng Sun, Gao Liu, Gang Liu, Yan Xiao
BACKGROUND: Multiple myeloma is a cancer which has a high occurrence rate and causes great injury to people worldwide. In recent years, many studies reported the effects of miRNA on the appearance of multiple myeloma. However, due to the differences of samples and sequencing platforms, a large number of inconsistent results have been generated among these studies, which limited the cure of multiple myeloma at the miRNA level. METHODS: We performed meta-analyses to identify the key miRNA biomarkers which could be applied on the treatment of multiple myeloma...
2017: PeerJ
https://www.readbyqxmd.com/read/28167700/the-transcription-factor-myb29-is-a-regulator-of-alternative-oxidase-1
#13
Xinhua Zhang, Aneta Ivanova, Klaas Vandepoele, Jordan D Radomiljac, Jan Van de Velde, Oliver Berkowitz, Patrick Willems, Yue Xu, Sophia Ng, Olivier Van Aken, Owen Duncan, Botao Zhang, Véronique Storme, Kai Xun Chan, Dries Vaneechoutte, Barry J Pogson, Frank Van Breusegem, James Whelan, Inge De Clercq
Plants sense and integrate a variety of signals from the environment through various interacting signal transduction pathways that involve hormones and signaling molecules. Using the ALTERNATIVE OXIDASE 1a (AOX1a) gene expression as a model system of retrograde or stress signaling between mitochondria and the nucleus, the MYB DOMAIN PROTEIN 29 (MYB29) was identified as a negative regulator (rao7 mutant) in a genetic screen of Arabidopsis thaliana. rao7/myb29 mutants have increased levels of AOX1a at a transcript and protein level after induction with antimycin A...
February 6, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28161101/prognostic-and-clinicopathological-value-of-nm23-expression-in-patients-with-breast-cancer-a-systematic-review-and-meta-analysis
#14
Wei Han, Cong Zhang, Fei-Yun Cao, Fang Cao, Lai Jiang, Hou-Zhong Ding
It is hypothesized that, NM23, as a metastasis suppressor gene, may be a good indicator of patients with breast cancer in most reports. The aim of our meta-analysis was to determine the prognostic value of NM23 in patients with breast cancer synthetically, by searching 3 databases, PubMed, EMBASE, and Web of Science, for relevant articles. The inclusion criteria, exclusion criteria, and the standard-of-quality assessment were used according to a previous protocol. The pooled odd ratios (ORs) and corresponding 95% CI were calculated to assess the primary end point, survival data, and the secondary end point, associations between NM23 expression and clinicopathological factors...
December 5, 2016: Current Problems in Cancer
https://www.readbyqxmd.com/read/28160555/oncofetal-gene-sall4-and-prognosis-in-cancer-a-systematic-review-with-meta-analysis
#15
Lorenzo Nicolè, Tiziana Sanavia, Nicola Veronese, Rocco Cappellesso, Claudio Luchini, Paolo Dabrilli, Ambrogio Fassina
The Spalt-Like Transcription Factor 4 (SALL4) oncogene plays a central function in embryo-fetal development and is absent in differentiated tissues. Evidence suggests that it can be reactivated in several cancers worsening the prognosis. We aimed at investigating the risk associated with SALL4 reactivation for all-cause mortality and recurrence in cancer using the current literature. A PubMed and SCOPUS search until 1st September 2016 was performed, focusing on perspective studies reporting prognostic parameters in cancer data...
February 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28158968/a-genome-wide-association-study-in-a-large-f2-cross-of-laying-hens-reveals-novel-genomic-regions-associated-with-feather-pecking-and-aggressive-pecking-behavior
#16
Vanessa Lutz, Patrick Stratz, Siegfried Preuß, Jens Tetens, Michael A Grashorn, Werner Bessei, Jörn Bennewitz
BACKGROUND: Feather pecking and aggressive pecking in laying hens are serious economic and welfare issues. In spite of extensive research on feather pecking during the last decades, the motivation for this behavior is still not clear. A small to moderate heritability has frequently been reported for these traits. Recently, we identified several single-nucleotide polymorphisms (SNPs) associated with feather pecking by mapping selection signatures in two divergent feather pecking lines...
February 3, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28158590/a-whole-blood-transcriptome-meta-analysis-identifies-gene-expression-signatures-of-cigarette-smoking
#17
Tianxiao Huan, Roby Joehanes, Claudia Schurmann, Katharina Schramm, Luke C Pilling, Marjolein J Peters, Reedik Mägi, Dawn DeMeo, George T O'Connor, Luigi Ferrucci, Alexander Teumer, Georg Homuth, Reiner Biffar, Uwe Völker, Christian Herder, Melanie Waldenberger, Annette Peters, Sonja Zeilinger, Andres Metspalu, Albert Hofman, André G Uitterlinden, Dena G Hernandez, Andrew B Singleton, Stefania Bandinelli, Peter J Munson, Honghuang Lin, Emelia J Benjamin, Tõnu Esko, Hans J Grabe, Holger Prokisch, Joyce B J van Meurs, David Melzer, Daniel Levy
No abstract text is available yet for this article.
November 1, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/28158196/transcriptome-wide-co-expression-analysis-identifies-lrrc2-as-a-novel-mediator-of-mitochondrial-and-cardiac-function
#18
Chris McDermott-Roe, Marion Leleu, Glenn C Rowe, Oleg Palygin, John D Bukowy, Judy Kuo, Monika Rech, Steffie Hermans-Beijnsberger, Sebastian Schaefer, Eleonora Adami, Esther E Creemers, Matthias Heinig, Blanche Schroen, Zoltan Arany, Enrico Petretto, Aron M Geurts
Mitochondrial dysfunction contributes to myriad monogenic and complex pathologies. To understand the underlying mechanisms, it is essential to define the full complement of proteins that modulate mitochondrial function. To identify such proteins, we performed a meta-analysis of publicly available gene expression data. Gene co-expression analysis of a large and heterogeneous compendium of microarray data nominated a sub-population of transcripts that whilst highly correlated with known mitochondrial protein-encoding transcripts (MPETs), are not themselves recognized as generating proteins either localized to the mitochondrion or pertinent to functions therein...
2017: PloS One
https://www.readbyqxmd.com/read/28157702/long-noncoding-rna-meg3-a-potential-novel-biomarker-to-predict-the-clinical-outcome-of-cancer-patients-a-meta-analysis
#19
Xiangrong Cui, Xuan Jing, Chunlan Long, Jie Tian, Jing Zhu
Numerous studies have demonstrated that the expression level of maternally expressed gene 3 (MEG3) was lost in various cancers. Low expression of MEG3 is associated with an increased risk of metastasis and a poor prognosis in cancer patients. This meta-analysis investigated the association between MEG3 levels and distant metastasis (DM), lymph node metastasis (LNM), overall survival (OS), and recurrence-free survival (RFS) of cancer patients. A total of 536 participants from 9 articles were finally enrolled...
February 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28152545/blood-based-micrornas-as-biomarkers-for-the-diagnosis-of-colorectal-cancer-a-systematic-review-and-meta-analysis
#20
Jane V Carter, Norman J Galbraith, Dongyan Yang, James F Burton, Samuel P Walker, Susan Galandiuk
BACKGROUND: Colorectal cancer (CRC) is common and associated with significant mortality. Current screening methods for CRC lack patient compliance. microRNAs (miRNAs), identified in body fluids, are negative regulators of gene expression and are dysregulated in many cancers, including CRC. This paper summarises studies identifying blood-based miRNAs dysregulated in CRC compared with healthy controls in an attempt to evaluate their use as a screening tool for the diagnosis of CRC. METHODS: A search of electronic databases (PubMed and EMBASE) and grey literature was performed between January 2002 and April 2016...
February 2, 2017: British Journal of Cancer
keyword
keyword
99501
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"