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Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

Andrew Williams, Sabina Halappanavar
2015 Beilstein Journal of Nanotechnology  
Several datasets from public microarray repositories describing pulmonary diseases in mouse models following exposure to a variety of substances were examined and functionally related biclusters of genes  ...  The identified biclusters were then used to conduct a gene set enrichment analysis on pulmonary gene expression profiles derived from mice exposed to nano-titanium dioxide (nano-TiO 2 ), carbon black (  ...  In the present study, we used a meta-analysis approach like that described by Turcan et al.  ... 
doi:10.3762/bjnano.6.252 pmid:26885455 pmcid:PMC4734442 fatcat:sppiohyjhfbzflgq6iyyylj4ga

Panel Data Methods and Applications to Health Economics [chapter]

Andrew M. Jones
2009 Palgrave Handbook of Econometrics  
This chapter reviews the data and methods that are used in applied health economics with a particular emphasis on the use of panel data.  ...  Models for longitudinal data 5.1 Applications of linear models 5.2 Applications with categorical outcomes 5.3 Applications with count data 5.4 Applications of quantile regression and other semiparametric  ...  For example Gallet and List (2003) present a meta-analysis of the tobacco price elasticity and Gemmill et al. (2007) carry out a meta-regression of estimates of the price elasticity of prescription  ... 
doi:10.1057/9780230244405_12 fatcat:4k3cr7zqwnegrdxaqm226mwj54

Comprehensive literature review and statistical considerations for microarray meta-analysis

George C. Tseng, Debashis Ghosh, Eleanor Feingold
2012 Nucleic Acids Research  
Here, we perform a systematic search from PubMed and manual collection to obtain 620 genomic meta-analysis papers, of which 333 microarray meta-analysis papers are summarized as the basis of this paper  ...  When the term 'microarray meta-analysis' is used, it usually means meta-analysis for DE gene (or marker) detection. Although two-thirds of identified publications Figure 1.  ...  Wang and G. Liao for collecting and printing papers.  ... 
doi:10.1093/nar/gkr1265 pmid:22262733 pmcid:PMC3351145 fatcat:qobv27m2rnbjfcsu2he6qkviuy

The Selection Strategy for Circulating Tumor Cells (CTCs) Isolation and Enumeration: Technical Features, Methods, and Clinical Applications [chapter]

Jason Chia-Hsun Hsieh, Tyler Ming-Hsien Wu
2016 Tumor Metastasis  
The key aim of the proposed chapter is to provide readers a brief description for the most important parts of the field of circulating tumor cells (CTCs): the core techniques, including negative and positive  ...  Most importantly, we will also review the clinical applications and important findings in clinical trials.  ...  [296] reported a meta-analysis conducted a computerized retrieval of literatures.  ... 
doi:10.5772/64812 fatcat:kusaq7fiffbw5iqnhfo65k5bmi

When Is Hub Gene Selection Better than Standard Meta-Analysis?

Peter Langfelder, Paul S. Mischel, Steve Horvath, Timothy Ravasi
2013 PLoS ONE  
The article also reports a comparison of meta-analysis techniques applied to gene expression data and presents novel R functions for carrying out consensus network analysis, network based screening, and  ...  However, standard meta-analysis methods perform as good as (if not better than) a consensus network approach in terms of validation success (criterion 2).  ...  Lusis, Art Arnold, and Roel Ophoff for their input. The mouse data were generated by the Lusis lab. Author Contributions Conceived and designed the experiments: PL PSM SH. Analyzed the data: PL.  ... 
doi:10.1371/journal.pone.0061505 pmid:23613865 pmcid:PMC3629234 fatcat:tyasp555ejgdnjd5mkzuzznh6u

Methods of Purification and Application Procedures of Alpha1 Antitrypsin: A Long-Lasting History

Simona Viglio, Paolo Iadarola, Maura D'Amato, Jan Stolk
2020 Molecules  
The aim of the present report is to review the literature addressing the methods developed for the purification of alpha1-antitrypsin (AAT) from the 1950s to the present.  ...  The lack of this inhibitor in human serum is responsible for the onset of alpha1-antitrypsin deficiency (AATD), which is a severe genetic disorder that affects lungs in adults and for which there is currently  ...  ., Pavia, for helpful discussion about the content of this chapter. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules25174014 pmid:32887469 fatcat:dy7edmjdnbb7parjyfkbwwcyau

A-MADMAN: Annotation-based microarray data meta-analysis tool

Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi
2009 BMC Bioinformatics  
Results: This work presents A-MADMAN, an open source web application which allows the retrieval, annotation, organization and meta-analysis of gene expression datasets obtained from Gene Expression Omnibus  ...  A-MADMAN addresses and resolves several open issues in the metaanalysis of gene expression data.  ...  A-MADMAN approach The purpose of this paper is to present A-MADMAN, an open source web application for the meta-analysis of Affymetrix data contained in Gene Expression Omnibus (GEO).  ... 
doi:10.1186/1471-2105-10-201 pmid:19563634 pmcid:PMC2711946 fatcat:vxdxzqfmznf5fkynvwzi5eyvdi

Quantitative trait loci: a meta-analysis

B Goffinet, S Gerber
2000 Genetics  
An application of the method is given using data from the maize database available online at http://www. agron.missouri.edu/.  ...  This article presents a method to combine QTL results from different independent analyses.  ...  A meta-analysis consists of combining data from dif-of qualitative developmental genes (Khavkin and Coe 1997, 1998) . ferent sources in a single study.  ... 
pmid:10790417 pmcid:PMC1461053 fatcat:q2m5nb3f7jhdnljfvzwtcwtpom

Regularized gene selection in cancer microarray meta-analysis

Shuangge Ma, Jian Huang
2009 BMC Bioinformatics  
The meta analysis of cancer microarray data is challenging because of the high dimensionality of gene expressions and the differences in experimental settings amongst different experiments.  ...  Results: We propose a Meta Threshold Gradient Descent Regularization (MTGDR) approach for gene selection in the meta analysis of cancer microarray data.  ...  We would like to thank three referees for very insightful comments which have led to significant improvement of this article.  ... 
doi:10.1186/1471-2105-10-1 pmid:19118496 pmcid:PMC2631520 fatcat:7iqmtbbn6veprfhmkzitt2pa6y

Avoiding pitfalls in gene (co)expression meta-analysis

Gabriel Östlund, Erik L.L. Sonnhammer
2014 Genomics  
Differential gene expression analysis between healthy and diseased groups is a widely used approach to understand the molecular underpinnings of disease.  ...  We performed a large scale comparative analysis of clinical expression data, using several background corrections and differential expression metrics.  ...  Surveys of published top lists of differentially expressed genes have shown a low degree of overlap between microarray expression studies for ovarian cancer [11] as well as between microarray expression  ... 
doi:10.1016/j.ygeno.2013.10.006 pmid:24184361 fatcat:ps7k6q5pgreoppzwhlnoqmsswa

Robust rank aggregation for gene list integration and meta-analysis

Raivo Kolde, Sven Laur, Priit Adler, Jaak Vilo
2012 Computer applications in the biosciences : CABIOS  
Prioritized gene lists are a common result presentation method in genomic data analysis applications.  ...  Our method detects genes that are ranked consistently better than expected under null hypothesis of uncorrelated inputs and assigns a significance score for each gene.  ...  DISCUSSION Gene expression meta-analysis The accumulation of gene expression studies has created a situation where one can pose new questions about the co-expression and functional role of genes by integrating  ... 
doi:10.1093/bioinformatics/btr709 pmid:22247279 pmcid:PMC3278763 fatcat:7sn45nzggnd5lofj5jfkzmcgyi

Meta-analysis of genetic association studies

Marcus R. Munafò, Jonathan Flint
2004 Trends in Genetics  
A survey of 600 positive associations between common gene variants and disease showed that most reported associations are not robust: of 166 associations that were studied three or more times, only six  ...  Meta-analysis, a statistical tool for combining results across studies, is becoming popular as a method for resolving discrepancies in genetic association studies.  ...  We suggest that meta-analysis can determine whether a real effect is present or not and we recommend its use to address this issue; at the same time, we hope that the application of meta-analysis does  ... 
doi:10.1016/j.tig.2004.06.014 pmid:15313553 fatcat:nt2cizxqwjdpfpkvnklnqvcc2u

Methods for transcriptomic analyses of the porcine host immune response: Application to Salmonella infection using microarrays

C.K. Tuggle, S.M.D. Bearson, J.J. Uthe, T.H. Huang, O.P. Couture, Y.F. Wang, D. Kuhar, J.K. Lunney, V. Honavar
2010 Veterinary Immunology and Immunopathology  
In this review, we describe these recent developments in the context of our work using primarily microarrays to explore gene expression changes during infection of pigs by Salmonella.  ...  Thus while the focus is not a comprehensive review of all possible approaches, we provide links and information on both the tools we use as well as alternatives commonly available for transcriptomic data  ...  None of these study sponsors had a role in writing or submission of this manuscript.  ... 
doi:10.1016/j.vetimm.2010.10.006 pmid:21036404 pmcid:PMC6545292 fatcat:4ysi5fzdarel7mbyflsiuevhcy

Meta-analysis of gene expression microarrays with missing replicates

Fan Shi, Gad Abraham, Christopher Leckie, Izhak Haviv, Adam Kowalczyk
2011 BMC Bioinformatics  
Results: We propose a meta-analysis framework, called "Incomplete Gene Meta-analysis", which can include incomplete genes by imputing the significance of missing replicates, and computing a meta-score  ...  Conclusions: Meta-analysis is an effective approach that identifies more robust sets of differentially expressed genes from multiple studies.  ...  An important application of gene expression microarrays is detecting differentially expressed genes by statistical analysis.  ... 
doi:10.1186/1471-2105-12-84 pmid:21435268 pmcid:PMC3224118 fatcat:fyxiljohyfcwfhxmp4zr6nzuvi

Integrative Meta-Analysis of Differential Gene Expression in Acute Myeloid Leukemia

Brady G. Miller, John A. Stamatoyannopoulos, Chad Creighton
2010 PLoS ONE  
A systematic comparison of the large body of gene expression profiling studies in AML has the potential to test the extensibility of conclusions based on single studies and provide further insights into  ...  Gene expression profiling studies of patients with AML has provided key insights into disease pathogenesis while exposing potential diagnostic and prognostic markers and therapeutic targets.  ...  Discussion We developed a methodology for the comparison of published heterogeneous gene lists, and we developed a web application (http://gat.stamlab.org) to facilitate access to the study data.  ... 
doi:10.1371/journal.pone.0009466 pmid:20209125 pmcid:PMC2830886 fatcat:cjy7i7ptxnajdffu4zwr5pq6fq
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