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Analysis of SNP-expression association matrices

A. Tsalenko, R. Sharan, H. Edvardsen, V. Kristensen, A.-L. Boerresen-Dale, A. Ben-Dor, Z. Yakhini
2005 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05)  
The framework consists of methods to associate transcripts with SNPs affecting their expression, algorithms to detect subsets of transcripts that share significantly many associations with a subset of  ...  In this paper we present a general statistical framework for the simultaneous analysis of gene expression data and SNP genotype data measured for the same cohort.  ...  Analysis of functional enrichment Gene sets that were associated to one or more SNPs were subjected to analysis of their functional enrichment based on their Gene Ontology (GO) annotations.  ... 
doi:10.1109/csb.2005.14 dblp:conf/csb/TsalenkoSEKBBY05 fatcat:l6adcs7b4bauph4cnxbocjecbq

ANALYSIS OF SNP-EXPRESSION ASSOCIATION MATRICES

ANYA TSALENKO, RODED SHARAN, VESSELA KRISTENSEN, HEGE EDVARDSEN, ANNE-LISE BØRRESEN-DALE, AMIR BEN-DOR, ZOHAR YAKHINI
2006 Journal of Bioinformatics and Computational Biology  
The framework consists of methods to associate transcripts with SNPs affecting their expression, algorithms to detect subsets of transcripts that share significantly many associations with a subset of  ...  In this paper we present a general statistical framework for the simultaneous analysis of gene expression data and SNP genotype data measured for the same cohort.  ...  Analysis of functional enrichment Gene sets that were associated to one or more SNPs were subjected to analysis of their functional enrichment based on their Gene Ontology (GO) annotations.  ... 
doi:10.1142/s0219720006001953 pmid:16819783 fatcat:wdsfunskavcpzebbr6xird5bw4

An application of matrix eQTL to billions hypothesis testing to identify expression quantitative trait loci in genome wide association studies of inflammatory bowel disease

Fahimeh Moradi, Morteza Hajihosseini, Elham Khodayari-Moez, Irina Dinu
2020 Journal of Cancer Prevention & Current Research  
Author contributions Conflicts of interest The authors have no conflicts of interest to declare for this study. Funding None.  ...  Most of the eQTL methods take days to complete the analysis. Matrix eQTL takes only a few minutes to run the analysis of SNP and gene expression associations in large datasets.  ...  Data matrices are sliced in blocks of up to 10,000 variables. Then gene expression and genotype matrices are standardized.  ... 
doi:10.15406/jcpcr.2020.11.00424 fatcat:iwzottnxhfbnxpd67omli4fkka

Matrix eQTL: Ultra fast eQTL analysis via large matrix operations [article]

Andrey A. Shabalin
2011 arXiv   pre-print
This makes the analysis computationally complex as it involves independent testing for association for every transcript-SNP pair.  ...  A modern eQTL dataset contains millions of SNPs and thousands of transcripts measured for hundreds of samples.  ...  The goal of eQTL analysis is to identify genomic locations where the genotype is significantly associated with expression of known genes.  ... 
arXiv:1105.5764v1 fatcat:fzis5rzozze3texdt36w4abpky

ICAM-1-related long non-coding RNA: promoter analysis and expression in human retinal endothelial cells

Amanda L. Lumsden, Yuefang Ma, Liam M. Ashander, Andrew J. Stempel, Damien J. Keating, Justine R. Smith, Binoy Appukuttan
2018 BMC Research Notes  
Five phenotype-associated single nucleotide polymorphisms (SNPs) in the immediate vicinity of these elements included four SNPs (i.e. rs2569693, rs281439, rs281440 and rs11575074) predicted to impact binding  ...  To address this issue, we undertook a comprehensive in silico analysis of the human ICR gene promoter region.  ...  Description of phenotype-nucleotide polymorphisms (SNPs) predicted to influence transcription of the human ICR gene. Table S4 .  ... 
doi:10.1186/s13104-018-3384-8 pmid:29743093 pmcid:PMC5944171 fatcat:zjlf5mj5g5hxhe2lw26djwa7ie

A distance-based test of association between paired heterogeneous genomic data

Christopher Minas, Edward Curry, Giovanni Montana
2013 Computer applications in the biosciences : CABIOS  
Compared to the classical Mantel test for association between distance matrices, the GRV test has been found to be more powerful in a number of simulation settings.  ...  We also demonstrate how the GRV test can be used to detect biological pathways in which genetic variability is associated to variation in gene expression levels in an ovarian cancer sample, and present  ...  These results suggest that the association between distance matrices based on the levels of expression of genes within certain pathways and distance matrices based on SNP genotypes associated with genes  ... 
doi:10.1093/bioinformatics/btt450 pmid:23918252 fatcat:sqk57za5fzczths2cndo5dwtzq

Improved estimation of SNP heritability using Bayesian multiple-phenotype models

Najla Saad Elhezzani
2018 European Journal of Human Genetics  
Linear mixed models (LMM) are widely used to estimate narrow sense heritability explained by tagged single-nucleotide polymorphisms (SNPs).  ...  The use of multivariate Bayesian methods allows us to circumvent some issues related to small sample sizes, mainly overfitting and boundary estimates.  ...  To this end, we repeated the analysis, excluding the SNPs previously associated with CHURC1 expression from the model, and the trace plots for its heritability appeared unstable using the same burn-in  ... 
doi:10.1038/s41431-018-0100-z pmid:29440776 fatcat:zisi3yxxkjdmznvmik5yaluweu

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

A. A. Shabalin
2012 Bioinformatics  
For modern datasets, eQTL analysis is a computationally intensive task as it involves testing for association of billions of transcript-SNP pair.  ...  Motivation: Expression quantitative trait loci (eQTL) analysis links variations in gene expression levels to genotypes.  ...  Cancer Institute (R01-CA138255), National Institute of Mental Health (R01-MH090936), and the Gillings Innovation Laboratory in Statistical Genomics.  ... 
doi:10.1093/bioinformatics/bts163 pmid:22492648 pmcid:PMC3348564 fatcat:v7tda7drfnffnabjhxhep7fzcq

A Distance-Based Test of Association Between Paired Heterogeneous Genomic Data [article]

Christopher Minas, Edward Curry, Giovanni Montana
2013 arXiv   pre-print
Compared to the classical Mantel test for association between distance matrices, the GRV test has been found to be more powerful in a number of simulation settings.  ...  We also report on an application of the GRV test to detect biological pathways in which genetic variability is associated to variation in gene expression levels in ovarian cancer samples, and present results  ...  Liu, Genome Institute of Singapore, and the Agency for Science Technology and Research of Singapore for use of ovarian cancer microarray data. E. C. was funded by Ovarian Cancer Action, and G.  ... 
arXiv:1303.7002v1 fatcat:svzxakue4vderf6vxxnotpaajm

Characterizing human genomic coevolution in locus-gene regulatory interactions

Daniel Savel, Mehmet Koyutürk
2019 BioData Mining  
Exploring this property we found that coevolution might be useful in prioritizing association tests in cis-eQTL detection.  ...  We characterize coevolution as it appears in locus-gene interactions in the human genome, focusing on expression Quantitative Trait - Locus (eQTL) interactions.  ...  This work was supported by the National Libraries of Medicine and the National Cancer Institute at the National Institutes of Health (grant numbers RO1-LM04127, U01-CA198941).  ... 
doi:10.1186/s13040-019-0195-y pmid:30923571 pmcid:PMC6419833 fatcat:kzx22izcobdlra4snchbay4yfi

Using Canonical Correlation Analysis to Discover Genetic Regulatory Variants

Melissa G. Naylor, Xihong Lin, Scott T. Weiss, Benjamin A. Raby, Christoph Lange, Anna Carla Goldberg
2010 PLoS ONE  
Such analyses typically involve a linkage or association analysis in which expression data are used as phenotypes.  ...  Discovering genetic associations between genetic markers and gene expression levels can provide insight into gene regulation and, potentially, mechanisms of disease.  ...  We acknowledge the CAMP investigators and research team, supported by NHLBI, for collection of CAMP Genetic Ancillary Study data.  ... 
doi:10.1371/journal.pone.0010395 pmid:20485529 pmcid:PMC2869348 fatcat:nflbnsoqujhu3m36x7vlcgzjly

A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition

Sarah E Harris, Helen Fox, Alan F Wright, Caroline Hayward, John M Starr, Lawrence J Whalley, Ian J Deary
2007 BMC Genetics  
An intronic SNP in the APP gene (rs2830102) was significantly associated with cognitive ageing in both LBC1921 and a combined LBC1921/ABC1936 analysis (p < 0.01), but not in ABC1936 alone.  ...  SNPs showing a significant positive association were then genotyped in a second cohort for whom we have cognitive ability scores at the ages of 11 and 64 years (ABC1936).  ...  (Continued)However, APP intronic SNP rs2830102 genotype was associated with non-verbal reasoning, as measured by Raven's Progressive Matrices, in a joint analysis of LBC1921 and ABC1936 data.  ... 
doi:10.1186/1471-2156-8-43 pmid:17601350 pmcid:PMC1933580 fatcat:bzf3zsxowvgedajhuosg5aadba

Identification of genes associated with complex traits by testing the genetic dissimilarity between individuals

Yan V Sun, Wei Zhao, Kerby A Shedden, Sharon LR Kardia
2011 BMC Proceedings  
genes with simulated genetic associations.  ...  The method is based on the Mantel test, which assesses the correlation between two distance matrices using a permutation procedure.  ...  The Genetic Analysis Workshops are supported by NIH grant R01 GM031575. This article has been published as part of BMC Proceedings Volume 5 Supplement 9, 2011: Genetic Analysis Workshop 17.  ... 
doi:10.1186/1753-6561-5-s9-s120 pmid:22373401 pmcid:PMC3287845 fatcat:bdasweo6kzfmtgmh3zofutc67e

Identifying regulatory relationships among genomic loci, biological pathways, and disease

Jung Hoon Woo, Sung Bum Cho, Eunjee Lee, Ju Han Kim
2010 Artificial Intelligence in Medicine  
SNP-pathway association analysis using principal component analysis Principal component analysis was used to summarize the expression of multiple genes for the pathways.  ...  SNP/single-gene association analysis For comparison with set-wise approaches, we also tested the association between a gene's expression level and a SNP for all SNP/ gene pairs.  ... 
doi:10.1016/j.artmed.2010.03.001 pmid:20554166 fatcat:wdhtjiortrfd5dcgb52lyj2uci

Leveraging Gene Co-expression Patterns to Infer Trait-Relevant Tissues in Genome-wide Association Studies [article]

Lulu Shang, Jennifer A. Smith, Xiang Zhou
2019 bioRxiv   pre-print
Genome-wide association studies (GWASs) have identified many SNPs associated with various common diseases.  ...  Understanding the biological functions of these identified SNP associations requires identifying disease/trait relevant tissues or cell types.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1101/705129 fatcat:mx4uegmjmrgfngspcpr7qjmsrm
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