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gene expression meta analysis

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https://www.readbyqxmd.com/read/28651018/meta-analysis-of-mirna-expression-profiles-for-prostate-cancer-recurrence-following-radical-prostatectomy
#1
Elnaz Pashaei, Elham Pashaei, Maryam Ahmady, Mustafa Ozen, Nizamettin Aydin
BACKGROUND: Prostate cancer (PCa) is a leading reason of death in men and the most diagnosed malignancies in the western countries at the present time. After radical prostatectomy (RP), nearly 30% of men develop clinical recurrence with high serum prostate-specific antigen levels. An important challenge in PCa research is to identify effective predictors of tumor recurrence. The molecular alterations in microRNAs are associated with PCa initiation and progression. Several miRNA microarray studies have been conducted in recurrence PCa, but the results vary among different studies...
2017: PloS One
https://www.readbyqxmd.com/read/28649742/genotranscriptomic-meta-analysis-of-the-chd-family-chromatin-remodelers-in-human-cancers-initial-evidence-of-an-oncogenic-role-for-chd7
#2
Xiaofang Chu, Xuhui Guo, Yuanyuan Jiang, Huimei Yu, Lanxin Liu, Wenqi Shan, Zeng-Quan Yang
Chromodomain helicase DNA binding proteins (CHD) are characterized by N-terminal tandem chromodomains and a central ATP-dependent helicase domain. CHDs govern the cellular machinery's access to DNA, thereby playing critical roles in various cellular processes including transcription, proliferation, and DNA damage repair. Accumulating evidence demonstrates that mutation and dysregulation of CHDs are implicated in the pathogenesis of developmental disorders and cancer. However, we know little about genomic and transcriptomic alterations and the clinical significance of most CHDs in human cancer...
June 26, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28649314/hierarchical-cortical-transcriptome-disorganization-in-autism
#3
Michael V Lombardo, Eric Courchesne, Nathan E Lewis, Tiziano Pramparo
BACKGROUND: Autism spectrum disorders (ASD) are etiologically heterogeneous and complex. Functional genomics work has begun to identify a diverse array of dysregulated transcriptomic programs (e.g., synaptic, immune, cell cycle, DNA damage, WNT signaling, cortical patterning and differentiation) potentially involved in ASD brain abnormalities during childhood and adulthood. However, it remains unclear whether such diverse dysregulated pathways are independent of each other or instead reflect coordinated hierarchical systems-level pathology...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28648455/kinetic-modelling-and-meta-analysis-of-the-b-subtilis-siga-regulatory-network-during-spore-germination-and-outgrowth
#4
O Ramaniuk, M Černý, L Krásný, J Vohradsky
This study describes the meta-analysis and kinetic modelling of gene expression control by sigma factor SigA of Bacillus subtilis during germination and outgrowth based on microarray data from 14 time points. The analysis computationally models the direct interaction among SigA, SigA-controlled sigma factor genes (sigM, sigH, sigD, sigX), and their target genes. Of the >800 known genes in the SigA regulon, as extracted from databases, 311 genes were analysed, and 190 were confirmed by the kinetic model as being controlled by SigA...
June 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28647924/comparative-expression-analysis-of-rice-and-arabidopsis-peroxiredoxin-genes-suggests-conserved-or-diversified-roles-between-the-two-species-and-leads-to-the-identification-of-tandemly-duplicated-rice-peroxiredoxin-genes-differentially-expressed-in-seeds
#5
Yun-Shil Gho, Sun-A Park, Sung-Ruyl Kim, Anil Kumar Nalini Chandran, Gynheung An, Ki-Hong Jung
BACKGROUND: Peroxiredoxins (PRXs) have recently been identified as plant antioxidants. Completion of various genome sequencing projects has provided genome-wide information about PRX genes in major plant species. Two of these -- Oryza sativa (rice) and Arabidopsis -- each have 10 PRX members. Although significant progress has been made in understanding their biological roles in Arabidopsis, those functions in rice, a model crop plant, have not been well studied. RESULTS: We performed a comparative expression analysis of rice and Arabidopsis PRXs...
December 2017: Rice
https://www.readbyqxmd.com/read/28647138/think-like-a-sponge-the-genetic-signal-of-sensory-cells-in-sponges
#6
REVIEW
Jasmine L Mah, Sally P Leys
A complex genetic repertoire underlies the apparently simple body plan of sponges. Among the genes present in poriferans are those fundamental to the sensory and nervous systems of other animals. Sponges are dynamic and sensitive animals and it is intuitive to link these genes to behaviour. The proposal that ctenophores are the earliest diverging metazoan has led to the question of whether sponges possess a 'pre-nervous' system or have undergone nervous system loss. Both lines of thought generally assume that the last common ancestor of sponges and eumetazoans possessed the genetic modules that underlie sensory abilities...
June 21, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28644133/prognostic-value-of-decreased-long-non-coding-rna-tusc7-expression-in-some-solid-tumors-a-systematic-review-and-meta-analysis
#7
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...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28642624/whole-exome-sequencing-to-identify-genetic-variants-associated-with-raised-atherosclerotic-lesions-in-young-persons
#8
James E Hixson, Goo Jun, Lawrence C Shimmin, Yizhi Wang, Guoqiang Yu, Chunhong Mao, Andrew S Warren, Timothy D Howard, Richard S Vander Heide, Jennifer Van Eyk, Yue Wang, David M Herrington
We investigated the influence of genetic variants on atherosclerosis using whole exome sequencing in cases and controls from the autopsy study "Pathobiological Determinants of Atherosclerosis in Youth (PDAY)". We identified a PDAY case group with the highest total amounts of raised lesions (n = 359) for comparisons with a control group with no detectable raised lesions (n = 626). In addition to the standard exome capture, we included genome-wide proximal promoter regions that contain sequences that regulate gene expression...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637422/optimal-alpha-reduces-error-rates-in-gene-expression-studies-a-meta-analysis-approach
#9
J F Mudge, C J Martyniuk, J E Houlahan
BACKGROUND: Transcriptomic approaches (microarray and RNA-seq) have been a tremendous advance for molecular science in all disciplines, but they have made interpretation of hypothesis testing more difficult because of the large number of comparisons that are done within an experiment. The result has been a proliferation of techniques aimed at solving the multiple comparisons problem, techniques that have focused primarily on minimizing Type I error with little or no concern about concomitant increases in Type II errors...
June 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28634715/regulatory-element-based-prediction-identifies-new-susceptibility-regulatory-variants-for-osteoporosis
#10
Shi Yao, Yan Guo, Shan-Shan Dong, Ruo-Han Hao, Xiao-Feng Chen, Yi-Xiao Chen, Jia-Bin Chen, Qing Tian, Hong-Wen Deng, Tie-Lin Yang
Despite genome-wide association studies (GWASs) have identified many susceptibility genes for osteoporosis, it still leaves a large part of missing heritability to be discovered. Integrating regulatory information and GWASs could offer new insights into the biological link between the susceptibility SNPs and osteoporosis. We generated five machine learning classifiers with osteoporosis-associated variants and regulatory features data. We gained the optimal classifier and predicted genome-wide SNPs to discover susceptibility regulatory variants...
June 20, 2017: Human Genetics
https://www.readbyqxmd.com/read/28633309/tmprss2-erg-gene-fusions-in-prostate-cancer-of-west-african-men-and-a-meta-analysis-of-racial-differences
#11
Cindy Ke Zhou, Denise Young, Edward D Yeboah, Sally B Coburn, Yao Tettey, Richard B Biritwum, Andrew A Adjei, Evelyn Tay, Shelley Niwa, Ann Truelove, Judith Welsh, James E Mensah, Robert N Hoover, Isabell A Sesterhenn, Ann W Hsing, Shiv Srivastava, Michael B Cook
The prevalence of TMPRSS2-ERG fusions in prostate cancer varies by race. However, such somatic aberration and its association with prognostic factors have neither been studied in a West African population nor been systematically reviewed in the context of racial differences. We used immunohistochemistry to assess ERG expression as the established surrogate of ERG fusion genes among 262 prostate cancer biopsies from the Ghana Prostate Study. Poisson regression with robust variance estimation provided prevalence ratios and 95% confidence intervals of ERG expression in relation to patients' characteristics...
June 12, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28629367/african-american-esophageal-squamous-cell-carcinoma-expression-profile-reveals-dysregulation-of-stress-response-and-detox-networks
#12
Hayriye Verda Erkizan, Kory Johnson, Svetlana Ghimbovschi, Deepa Karkera, Gregory Trachiotis, Houtan Adib, Eric P Hoffman, Robert G Wadleigh
BACKGROUND: Esophageal carcinoma is the third most common gastrointestinal malignancy worldwide and is largely unresponsive to therapy. African-Americans have an increased risk for esophageal squamous cell carcinoma (ESCC), the subtype that shows marked variation in geographic frequency. The molecular architecture of African-American ESCC is still poorly understood. It is unclear why African-American ESCC is more aggressive and the survival rate in these patients is worse than those of other ethnic groups...
June 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28626070/potential-susceptibility-loci-identified-for-renal-cell-carcinoma-by-targeting-obesity-related-genes
#13
Xiang Shu, Mark P Purdue, Yuanqing Ye, Huakang Tu, Christopher G Wood, Nizar M Tannir, Zhaoming Wang, Demetrius Albanes, Susan M Gapstur, Victoria L Stevens, Nathaniel Rothman, Stephen J Chanock, Xifeng Wu
BACKGROUND: Obesity is an established risk factor for renal cell carcinoma (RCC). Although genome-wide association studies (GWAS) of RCC have identified several susceptibility loci, additional variants might be missed due to the highly conservative selection. METHODS: We conducted a multiphase study utilizing three independent genome-wide scans at MD Anderson Cancer Center (MDA RCC GWAS and MDA RCC OncoArray) and National Cancer Institute (NCI RCC GWAS), which consisted of a total of 3,530 cases and 5,714 controls, to investigate genetic variations in obesity-related genes and RCC risk...
June 16, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28623542/identification-of-differentially-expressed-mirnas-associated-with-chronic-kidney-disease-mineral-bone-disorder
#14
Kyung Im Kim, Sohyun Jeong, Nayoung Han, Jung Mi Oh, Kook-Hwan Oh, In-Wha Kim
The purpose of this study is to characterize a meta-signature of differentially expressed mRNA in chronic kidney disease (CKD) to predict putative microRNA (miRNA) in CKD-mineral bone disorder (CKD-MBD) and confirm the changes in these genes and miRNA expression under uremic conditions by using a cell culture system. PubMed searches using MeSH terms and keywords related to CKD, uremia, and mRNA arrays were conducted. Through a computational analysis, a meta-signature that characterizes the significant intersection of differentially expressed mRNA and expected miRNAs associated with CKD-MBD was determined...
June 14, 2017: Frontiers of Medicine
https://www.readbyqxmd.com/read/28623401/biomarkers-in-the-assessment-of-oral-mucositis-in-head-and-neck-cancer-patients-a-systematic-review-and-meta-analysis
#15
REVIEW
Ana Gabriela Costa Normando, Camila Lopes Rocha, Isabela Porto de Toledo, Paulo Tadeu de Souza Figueiredo, Paula Elaine Diniz Dos Reis, Graziela De Luca Canto, Eliete Neves Silva Guerra
PURPOSE: The aim of this study was to evaluate the capability of biomarkers to predict the risk of oral mucositis in head and neck cancer patients, as well as to assess the correlation between these biomarkers and the severity of mucositis. METHODS: The search was performed at LILACS, PubMed, Science Direct, Scopus, and Web of Science. A search of the gray literature was performed on Google Scholar, OpenGrey, and ProQuest. The methodological quality of the included studies was assessed using the Meta-Analysis of Statistics Assessment and Review Instrument (MAStARI) tool, and the evidence quality was assessed by the Grading of Recommendation, Assessment, Development, and Evaluation (GRADE) system...
June 16, 2017: Supportive Care in Cancer: Official Journal of the Multinational Association of Supportive Care in Cancer
https://www.readbyqxmd.com/read/28617547/mastl-is-a-potential-poor-prognostic-indicator-in-er-breast-cancer
#16
B-Z Zhuge, B-R Du, X-L Meng, Y-Q Zhang
OBJECTIVE: In this study, we aimed to explore prognostic value of MASTL (microtubule-associated serine/threonine kinase-like) in breast cancer patients on the basis of ER status and molecular subtypes. MATERIALS AND METHODS: The raw microarray data (GDS5666) of 4T1 derived bone-aggressive explant and primary tumor explant were reanalyzed to identify the dysregulated genes. To pool previous annotated genomic data that assessed the association between MASTL expression and metastatic relapse (MR) risk, MR-free survival, any event (AE, defined as any relapse or death) risk, and AE-free survival in breast cancer patients, a meta-analysis was performed by bc-GenExMiner 4...
May 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28611796/identification-of-important-physiological-traits-and-moderators-that-are-associated-with-improved-salt-tolerance-in-cbl-and-cipk-overexpressors-through-a-meta-analysis
#17
Yuanchun Ma, Qunkang Cheng, Zongming Cheng, Hui Li, Youhong Chang, Jing Lin
The CBL-CIPK pathway is a plant-specific Ca(2+) sensor relaying pathway that has been shown to be involved in plant response to salt stress. Over-expression of CBL-CIPK network genes has been reported to increase salt tolerance in many studies. The studies on the overexpression of CBL-CIPK network genes, however, have used various indices to evaluate the effect of these genes on salt tolerance and have indicated a variety of roles for the major CBL-CIPK pathway genes. Therefore, it is of great interest to analyze the various effects resulting from the overexpression CBL-CIPK pathway genes and their relation to salt tolerance...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28611791/regional-association-analysis-of-metaqtls-delineates-candidate-grain-size-genes-in-rice
#18
Anurag V Daware, Rishi Srivastava, Ashok K Singh, Swarup K Parida, Akhilesh K Tyagi
Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28610557/integration-of-quantitated-expression-estimates-from-polya-selected-and-rrna-depleted-rna-seq-libraries
#19
Stephen J Bush, Mary E B McCulloch, Kim M Summers, David A Hume, Emily L Clark
BACKGROUND: The availability of fast alignment-free algorithms has greatly reduced the computational burden of RNA-seq processing, especially for relatively poorly assembled genomes. Using these approaches, previous RNA-seq datasets could potentially be processed and integrated with newly sequenced libraries. Confounding factors in such integration include sequencing depth and methods of RNA extraction and selection. Different selection methods (typically, either polyA-selection or rRNA-depletion) omit different RNAs, resulting in different fractions of the transcriptome being sequenced...
June 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28606167/rdml-a-mathematica-package-for-parsing-and-importing-real-time-qpcr-data
#20
Ramiro Magno, Isabel Duarte, Raquel P Andrade, Isabel Palmeirim
OBJECTIVE: The purpose and objective of the research presented is to provide a package for easy importing of Real-Time PCR data markup language (RDML) data to Mathematica. RESULTS: Real-Time qPCR is the most widely used experimental method for the accurate quantification of gene expression. To enable the straightforward archiving and sharing of qPCR data and its associated experimental information, an XML-based data standard was developed-the Real-Time PCR data markup language (RDML)-devised by the RDML consortium...
June 12, 2017: BMC Research Notes
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