Continued development of an application for generation of phenotypic prototypes using simulated annealing (SAModk-prototypes). The application uses k-mode and k-means style clustering of categorical histopathology observations and numeric gene expression and clinical chemistry data respectively via simulated annealing optimization to cluster biological samples into groups which share phenotypic responses to stimuli. The clustering of the samples using SAModk-prototypes and all the data together performs better than clustering of the data using any one of the data domains separately or pairwise combinations of the data. -------------------------------------------------------------------------------------------------- Continued development of a software for biclustering of gene expression data using phenotypic measurements to constraint the clustering of the genes or by unsupervised clustering. The biclusters are phenotypically anchored to the gene expression. Constraining the clusters by Gene Onology biological processes was investigated. -------------------------------------------------------------------------------------------------- Performed analysis of next generation mRNA-Seq data. -------------------------------------------------------------------------------------------------- Continued development of computational means to analyze the S. pombe (yeast) genome across multiple time series experiments and to find transcription factor-gene regulatory units. -------------------------------------------------------------------------------------------------- Initiated an implemenation of genetical genomics (eQTL) data analysis using microarray gene expression data and genotype data.

Project Start
Project End
Budget Start
Budget End
Support Year
4
Fiscal Year
2010
Total Cost
$954,726
Indirect Cost
City
State
Country
Zip Code
Lozoya, Oswaldo A; Martinez-Reyes, Inmaculada; Wang, Tianyuan et al. (2018) Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation. PLoS Biol 16:e2005707
Duncan, Christopher G; Kondilis-Mangum, Hrisavgi D; Grimm, Sara A et al. (2018) Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells. G3 (Bethesda) 8:805-813
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Muñoz, M D; Della Vedova, M C; Bushel, P R et al. (2018) The nitrone spin trap 5,5-dimethyl-1-pyrroline N-oxide dampens lipopolysaccharide-induced transcriptomic changes in macrophages. Inflamm Res 67:515-530
Osgood, Ross S; Upham, Brad L; Bushel, Pierre R et al. (2017) Secondhand Smoke-Prevalent Polycyclic Aromatic Hydrocarbon Binary Mixture-Induced Specific Mitogenic and Pro-inflammatory Cell Signaling Events in Lung Epithelial Cells. Toxicol Sci 157:156-171
Funderburk, Karen M; Auerbach, Scott S; Bushel, Pierre R (2017) Crosstalk between Receptor and Non-receptor Mediated Chemical Modes of Action in Rat Livers Converges through a Dysregulated Gene Expression Network at Tumor Suppressor Tp53. Front Genet 8:157
Bennett, Brian D; Bushel, Pierre R (2017) goSTAG: gene ontology subtrees to tag and annotate genes within a set. Source Code Biol Med 12:6
Bushel, P R; Fannin, R D; Gerrish, K et al. (2017) Blood gene expression profiling of an early acetaminophen response. Pharmacogenomics J 17:230-236

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