Genomes and Genes
Kenneth F Manly
Affiliation: University of Tennessee
- Reliability of statistical associations between genes and diseaseKenneth F Manly
Pathology and Laboratory Medicine, Anatomy and Neurobiology, Center of Genomics and Bioinformatics, University of Tennessee Health Science Center, Memphis, USA
Immunogenetics 57:549-58. 2005..Three intervening classes, described as second-, third-, and fourth-class associations, are defined by P values separated by factors of 20 or 25 from these extremes...
- Weighting by heritability for detection of quantitative trait loci with microarray estimates of gene expressionKenneth F Manly
Department of Pathology, University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, TN 38163, USA
Genome Biol 6:R27. 2005..This heritability varies greatly. We have tested heritability-weighted averages to define expression of a transcript and found that these allow detection of more QTLs than previously described methods...
- Genomics, prior probability, and statistical tests of multiple hypothesesKenneth F Manly
Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
Genome Res 14:997-1001. 2004
- Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traitsHongqiang Li
Department of Molecular Sciences, University of Tennessee Health Science Center, 858 Madison Avenue Memphis, TN 38163, USA
Hum Mol Genet 15:481-92. 2006....
- Genetic networks controlling retinal injuryFelix R Vazquez-Chona
Department of Ophthalmology, The Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
Mol Vis 11:958-70. 2005..The present study defines genomic loci underlying coordinate changes in gene expression following retinal injury...
- Inferring gene transcriptional modulatory relations: a genetical genomics approachHongqiang Li
Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
Hum Mol Genet 14:1119-25. 2005..SNPs that distinguish between the two progenitor strains were used to further winnow the list of candidate modulators. Bayesian network was then used to identify the genetic modulatory relations that best explain the microarray data...
- Genetic correlates of gene expression in recombinant inbred strains: a relational model system to explore neurobehavioral phenotypesElissa J Chesler
Department of Anatomy and Neurobiology, Center for Genomics and Bioinformatics, University of Tennessee Health Science Center, Memphis, TN, USA
Neuroinformatics 1:343-57. 2003..By repeatedly studying the same panel of mice, early data can be re-examined in light of technological advances unforeseen at the time of their initial collection...
- WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behaviorElissa J Chesler
Department of Anatomy and Neurobiology, Center for Genomics and Bioinformatics, University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, Tennessee 38163, USA
Nat Neurosci 7:485-6. 2004
- How replicable are mRNA expression QTL?Jeremy L Peirce
Center for Neuroscience, Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
Mamm Genome 17:643-56. 2006..Finally, we note that while trans-acting QTL do not replicate well between data sets in general, at least one cluster of trans-acting QTL on distal Chr 1 is notably preserved between data sets...
- Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system functionElissa J Chesler
University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, Tennessee 38163, USA
Nat Genet 37:233-42. 2005..We built these tools into an open web resource called WebQTL that can be used to test a broad array of hypotheses...
- An ENU-induced mutation in Rs1h causes disruption of retinal structure and functionMonica M Jablonski
Department of Ophthalmology, University of Tennessee Health Science Center and Tennessee Mouse Genome Consortium, Memphis, TN, USA
Mol Vis 11:569-81. 2005..Herein we present its retinal phenotype and genetic basis...
- WebQTL: web-based complex trait analysisJintao Wang
Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
Neuroinformatics 1:299-308. 2003..A search function finds correlations between RNA expression and biological traits, and mapping functions find QTLs for either type of trait. The WebQTL service is available at http://www.webqtl.org/...
- Informatics center for mouse genomics: the dissection of complex traits of the nervous systemGlenn D Rosen
Department of Neurology, Division of Behavioral Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
Neuroinformatics 1:327-42. 2003..Finally, WebQTL provides statistical and graphical analysis of linkage between phenotypes and genotypes...
- Quantitative trait locus analysis using recombinant inbred intercrosses: theoretical and empirical considerationsFei Zou
Department of Biostatistics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
Genetics 170:1299-311. 2005....
- Genome-level analysis of genetic regulation of liver gene expression networksDaniel Gatti
Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
Hepatology 46:548-57. 2007..genenetwork.org) that allows custom data mining, identification of coregulated transcripts and correlated phenotypes, cross-tissue, and cross-species comparisons, as well as testing of a broad array of hypotheses...
- The nature and identification of quantitative trait loci: a community's viewOduola Abiola
Nat Rev Genet 4:911-6. 2003..Quantitative trait loci (QTLs) can be identified in several ways, but is there a definitive test of whether a candidate locus actually corresponds to a specific QTL?..
- Combined expression trait correlations and expression quantitative trait locus mappingHong Lan
Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
PLoS Genet 2:e6. 2006..The combined analysis is more sensitive compared with linkage mapping alone...
- Conventional P-values fail to assure reproducibility for genetic association testsKenneth F Manly
Trends Genet 21:268-9; author reply 269-71. 2005
- Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'Leonid Bystrykh
Department of Stem Cell Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
Nat Genet 37:225-32. 2005..Our data are accessible through WebQTL, a web-based interface that allows custom genetic linkage analysis and identification of coregulated transcripts...
- An informatics approach to systems neurogeneticsGlenn D Rosen
Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
Methods Mol Biol 401:287-303. 2007..Taken together, these tools enable the user to begin to assess complex interactions of gene networks, and facilitate analysis of traits using a systems approach...