Genomes and Genes
Affiliation: University of Alabama at Birmingham
- Design and validation issues in RNA-seq experimentsZhide Fang
Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, USA
Brief Bioinform 12:280-7. 2011..In this review, we use RNA-seq as an example to bring this topic into focus and to discuss experimental design and validation issues pertaining to next-generation sequencing in the quantification of transcripts...
- Inheritance patterns of transcript levels in F1 hybrid miceXiangqin Cui
Department of Biostatistics, Section on Statistical Genetics, Department of Medicine, Genetic and Translational Medicine Division, University of Alabama, Alabama 35294, USA
Genetics 174:627-37. 2006..In addition, we identified 314 transcripts with expression levels that differ between the reciprocal F1 animals. These genes may be related to maternal effect...
- Evaluation of a statistical equivalence test applied to microarray dataJing Qiu
Department of Statistics, University of Missouri, Columbia, Missouri, USA
J Biopharm Stat 20:240-66. 2010..We also compare the ROC curves of the equivalence test with those of the naive method of selecting genes that are not statistically significant DE...
- Kidney injury accelerates cystogenesis via pathways modulated by heme oxygenase and complementJuling Zhou
Department of Medicine, University of Alabama at Birmingham, USA
J Am Soc Nephrol 23:1161-71. 2012....
- Microarray data analysis: from disarray to consolidation and consensusDavid B Allison
Section on Statistical Genetics, Department of Biostatistics, Ryals Public Health Building, 1665 University Avenue, University of Alabama at Birmingham, Alabama 35294 0022, USA
Nat Rev Genet 7:55-65. 2006..Many are special cases of more general models, and points of consensus are emerging about the general approaches that warrant use and elaboration...
- Consistency analysis of redundant probe sets on affymetrix three-prime expression arrays and applications to differential mRNA processingXiangqin Cui
Department of Biostatistics, University of Alabama, Birmingham, Alabama, United States of America
PLoS ONE 4:e4229. 2009..This work demonstrates how P/A-call and genome-based filtering can improve consistency among redundant probe sets while at the same time exposing possible differential regulation of RNA processing pathways across sample types...
- Gene expression patterns in peripheral blood cells associated with radiographic severity in African Americans with early rheumatoid arthritisRichard J Reynolds
Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, 1530 3rd Avenue South, SHEL 178, Birmingham, AL 35294 2182, USA
Rheumatol Int 33:129-37. 2013....
- Renal CD14 expression correlates with the progression of cystic kidney diseaseJuling Zhou
Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
Kidney Int 78:550-60. 2010..But the association was significant when the analysis was confined to males. Clearly more studies need to be done to evaluate the utility of CD14 as a marker for outcomes in ADPKD...
- Validation of endogenous internal real-time PCR controls in renal tissuesXiangqin Cui
Department of Medicine, University of Alabama at Birmingham, 1900 University Blvd, Tinsley Harrison Tower 611J, Birmingham, AL 35294, USA
Am J Nephrol 30:413-7. 2009..Unfortunately, none of these controls fulfills this premise across a wide range of experimental conditions; consequently, none of them can be recommended for universal use...
- The effect of insulin on expression of genes and biochemical pathways in human skeletal muscleXuxia Wu
Department of Nutrition Sciences, University of Alabama at Birmingham, 1675 University Boulevard, Birmingham, AL 35294 3360, USA
Endocrine 31:5-17. 2007..The role of NGFI-B (NR4A1) as a new potential mediator of insulin action highlights the need for greater understanding of nuclear transcription factors in insulin action...
- Genes and biochemical pathways in human skeletal muscle affecting resting energy expenditure and fuel partitioningXuxia Wu
Dept of Nutrition Sciences, The Univ of Alabama at Birmingham, 1675 University Blvd, Birmingham, AL 35294 3360, USA
J Appl Physiol 110:746-55. 2011..Individual variations in whole body REE and RQ are regulated by differential expressions of specific genes and pathways intrinsic to skeletal muscle...
- Dynamic molecular and histopathological changes in the extracellular matrix and inflammation in the transition to heart failure in isolated volume overloadYuan wen Chen
Center for Heart Failure Research, Division of Cardiology, Univ of Alabama at Birmingham, 434 BMR2, 1530 3rd Ave S, Birmingham, AL 35294 2180, USA
Am J Physiol Heart Circ Physiol 300:H2251-60. 2011..In VO, an early phase of inflammation subsides at 5 wk but reappears at 15 wk with marked periostin production along with the suppression of genes related to PPAR-α and energy metabolism...
- Length bias correction for RNA-seq data in gene set analysesLiyan Gao
Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Bioinformatics 27:662-9. 2011..Since transcript length is not related to gene expression, adjusting for such length dependency in GSA becomes necessary...
- Single nucleotide polymorphisms affect both cis- and trans-eQTLsLang Chen
Department of Biostatistics, Section on Statistical Genetics, School of Public Health, University of Alabama at Birmingham, AL 35209, USA
Genomics 93:501-8. 2009..These results indicate that SNPs do affect both probe set summaries and eQTLs (both cis and trans), thus SNP-containing probes should be filtered out to improve the performance of eQTL mapping...
- Methods for nutrigenomics and longevity studies in Drosophila: effects of diets high in sucrose, palmitic acid, soy, or beefJiatao Ye
Department of Environmental Health Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
Methods Mol Biol 371:111-41. 2007..The significance of these results and other types of nutrigenomics and longevity analyses is discussed...
- Group B Streptococcus (GBS) urinary tract infection involves binding of GBS to bladder uroepithelium and potent but GBS-specific induction of interleukin 1alphaGlen C Ulett
Departments of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
J Infect Dis 201:866-70. 2010..Thus, binding of uropathogenic GBS to uroepithelium and vigorous induction of interleukin 1alpha represents the initial stages of GBS urinary tract infection...
- Differential genomic responses in old vs. young humans despite similar levels of modest muscle damage after resistance loadingAnna E Thalacker-Mercer
Department of Physiology and Biophysics, University of Alabama at Birmingham, Birmingham, AL 35294 0005, USA
Physiol Genomics 40:141-9. 2010....
- Improved statistical tests for differential gene expression by shrinking variance components estimatesXiangqin Cui
The Jackson Laboratory, Bar Harbor, Maine 04609, USA
Biostatistics 6:59-75. 2005..Thus FS provides a powerful and robust approach to test differential expression of genes that utilizes information not available in individual gene testing approaches and does not suffer from biases of the pooled variance approach...
- Analysis of the wheat endosperm transcriptomeDebbie L Laudencia-Chingcuanco
Western Regional Research Center, USDA ARS Buchanan Street, Albany, CA 94710, USA
J Appl Genet 47:287-302. 2006..Approximately 61% of the endosperm ESTs has been tentatively mapped in the hexaploid wheat genome. Using microarrays for global RNA profiling, we identified endosperm genes that are specifically up regulated in the developing grain...
- Exploration of low-dose estrogen effects: identification of No Observed Transcriptional Effect Level (NOTEL)Edward K Lobenhofer
National Center for Toxicogenomics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
Toxicol Pathol 32:482-92. 2004..For example, in the development of therapeutic drugs, a NOTEL could be used to identify doses of pharmaceutical compounds that are no longer effective at modulating the expression of biomarkers of efficacy...
- Statistical tests for differential expression in cDNA microarray experimentsXiangqin Cui
The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
Genome Biol 4:210. 2003..With more than two conditions, analysis of variance (ANOVA) can be used, and the mixed ANOVA model is a general and powerful approach for microarray experiments with multiple factors and/or several sources of variation...