Gene Expression

Datasets Available to Download ( alphabetical order by first author )

Liver expression of B6.C3H-6T (6T) (congenic mice with low serum IGF-1) and C57BL/6J mice

Ackert-Bicknell CL, Demissie S, Marín de Evsikova C, Hsu YH, DeMambro VE, Karasik D, Cupples LA, Ordovas JM, Tucker KL, Cho K, Canalis E, Paigen B, Churchill GA, Forejt J, Beamer WG, Ferrari S, Bouxsein ML, Kiel DP, Rosen CJ.
PPARG by dietary fat interaction influences bone mass in mice and humans
J Bone Miner Res. 2008 Sep; 23(9):1398-408. PMCID: PMC2683155 [ Full Text ]

Femurs of C57BL/6J and C3H/HeJ mice on low fat diet or low fat with Rosiglitazone diet [ login ]

Ackert-Bicknell CL, Shockley KR, Horton LG, Lecka-Czernik B, Churchill GA, Rosen CJ.
Strain-specific effects of rosiglitazone on bone mass, body composition, and serum insulin-like growth factor-I
Endocrinology. 2009 Mar;150(3):1330-40. PMCID: PMC2654751 [ Full Text ]

Gene expression patterns in the hippocampus and amygdala of endogenous depression and chronic stress models

Andrus BM, Blizinsky K, Vedell PT, Dennis K, Shukla PK, Schaffer DJ, Radulovic J, Churchill GA, Redei EE.
Gene expression patterns in the hippocampus and amygdala of endogenous depression and chronic stress models
Mol Psychiatry. 2012 Jan;17(1):49-61. PMCID: PMC3117129 [ Full Text ]

Inheritance patterns of transcript levels in F1 hybrid mice

Cui X, Affourtit J, Shockley KR, Woo Y, Churchill GA.
Inheritance patterns of transcript levels in f1 hybrid mice
Genetics. 2006 Oct;174(2):627-37. PMCID: PMC1602077. [ Full Text ]

Uncovering Genes and Regulatory Pathways Related to Urinary Albumin Excretion

Hageman RS, Leduc MS, Caputo CR, Tsaih SW, Churchill GA, Korstanje R.
Uncovering Genes and Regulatory Pathways Related to Urinary Albumin Excretion
J Am Soc Nephrol. 2011 Jan;22(1):73-81. PMCID: PMC3014036 [ Full Text ]

Hageman RS, Leduc MS, Korstanje R, Paigen B, Churchill GA.
A Bayesian Framework for Inference of the Genotype-Phenotype Map for Segregating Populations
Genetics. 2011 Apr;187(4):1163-70. PMCID: PMC3070524 [ Full Text ]

High-fat diet leads to tissue-specific changes reflecting risk factors for diseases in DBA/2J mice

Hageman RS, Wagener A, Hantschel C, Svenson KL, Churchill GA, Brockmann GA.
High fat diet leads to tissue specific changes reflecting risk factors for diseases in DBA/2J mice
Physiol Genomics. 2010 Jun;42(1):55-66. PMCID: PMC2888560 [ Full Text ]

Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors

Herschkowitz JI, Simin K, Weigman VJ, Mikaelian I, Usary J, Hu Z, Rasmussen KE, Jones LP, Assefnia S, Chandrasekharan S, Backlund MG, Yin Y, Khramtsov AI, Bastein R, Quackenbush J, Glazer RI, Brown PH, Green JE, Kopelovich L, Furth PA, Palazzo JP, Olopade OI, Bernard PS, Churchill GA, Van Dyke T, Perou CM.
Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
Genome Biol. 2007;8(5):R76. PMCID: PMC1929138 [ Full Text ]

Gene expression in 2,3,7,8-tetrachlordibenzo- p-dioxin (TCDD) drug-treated and control human hepatoma HepG2 cell lines

Kerr MK, Afsharie CA, Bennett L, Bushel P, Martinez J, Walker N, Churchill GA.
Statistical analysis of a gene expression microarray experiment with replication
Statistica Sinica 2002;12:203-218. [ Full Text ]

Dye-swap experiment: Liver gene expression in NZO/HlLt mice with CL316,243, a beta-3 adrenergic receptor agonist supplemented diet

Kerr MK, Leiter EH, Picard L, Churchill GA.
Sources of Variation in Microarray Experiments
(2006)
In: Computational and Statistical Approaches to Genomics, 2nd Edition.
Zhang W, Shmulevich I (eds). Kluwer Academic Publishers. pp 37-48. [ Springer ] [ Amazon ]

Two designed experiments (latin square and reference sample) that used independent arrays to study the same tissue samples

Kerr MK, Martin M, Churchill GA.
Analysis of variance for gene expression microarray data
J Comput Biol. 2000;7(6):819-37.

Genetic variation in Glp1r expression influences the rate of gastric emptying

Kumar KG, Byerley LO, Volaufova J, Drucker DJ, Churchill GA, Li R, York B, Zuberi A, Richards BK.
Genetic variation in Glp1r expression influences the rate of gastric emptying in mice
Am J Physiol Regul Integr Comp Physiol. 2008 Feb;294(2):R362-71. [ Full Text ]

PPARgamma2 gene expression signature in U-33 / gamma2 and U-33/c mouse cell lines

Lecka-Czernik B, Ackert-Bicknell C, Adamo ML, Marmolejos V, Churchill GA, Shockley KR, Reid IR, Grey A, Rosen CJ.
Activation of peroxisome proliferator-activated receptor gamma (PPARgamma) by rosiglitazone suppresses components of the insulin-like growth factor regulatory system in vitro and in vivo
Endocrinology. 2007 Feb;148(2):903-11.PMCID: PMC1851001 [ Full Text ]

Shockley KR, Lazarenko OP, Czernik PJ, Rosen CJ, Churchill GA, Lecka-Czernik B.
PPARgamma2 nuclear receptor controls multiple regulatory pathways of osteoblast differentiation from marrow mesenchymal stem cells
J Cell Biochem. 2009 Feb 1;106(2):232-46. PMCID: PMC2745312 [ Full Text ]

Shockley KR, Rosen CJ, Churchill GA, Lecka-Czernik B.
PPARgamma2 Regulates a Molecular Signature of Marrow Mesenchymal Stem Cells
PPAR Res. 2007;2007:81219. PMCID: PMC2234088 [ Full Text ]

Differential expression in a C57BL/6J-chrYA congenic strain versus its C57BL/6J background genotype in myocardial cells

Llamas B, Verdugo RA, Churchill GA, Deschepper CF.
Chromosome Y variants from different inbred mouse strains are linked to differences in the morphologic and molecular responses of cardiac cells to postpubertal testosterone
BMC Genomics. 2009 Apr 7;10:150. PMCID: PMC2679052 [ Full Text ]

Verdugo RA, Deschepper CF, Muñoz G, Pomp D, Churchill GA.
Importance of randomization in microarray experimental designs with Illumina platforms
Nucleic Acids Res. 2009 Sep;37(17):5610-8. PMCID: PMC2761262. [ Full Text ]

Exploration of low-dose estrogen effects: identification of No Observed Transcriptional Effect Level (NOTEL)

Lobenhofer EK, Cui X, Bennett L, Cable PL, Merrick BA, Churchill GA, Afshari CA.
Exploration of low-dose estrogen effects: identification of No Observed Transcriptional Effect Level (NOTEL)
Toxicol Pathol. 2004 Jul-Aug;32(4):482-92.

Temporal gene expression differences in mouse brain during sleep

Mackiewicz M, Shockley KR, Romer MA, Galante RJ, Zimmerman JE, Naidoo N, Baldwin DA, Jensen ST, Churchill GA, Pack AI.
Macromolecule biosynthesis: a key function of sleep
Physiol Genomics. 2007 Nov 14;31(3):441-57. [ Full Text ]

Overexpression of innate immune response genes in a model of recessive polycystic kidney disease

Mrug M, Zhou J, Woo Y, Cui X, Szalai AJ, Novak J, Churchill GA, Guay-Woodford LM.
Overexpression of innate immune response genes in a model of recessive polycystic kidney disease
Kidney Int. 2008 Jan;73(1):63-76.

Gene expression analysis of B.A chromosome substitution strains

Shockley KR, Churchill GA.
Gene expression analysis of mouse chromosome substitution strains
Mamm Genome. 2006 Jun;17(6):598-614.

Gene expression and proteomics analysis from a NZB X SM F2 cross

Stylianou IM, Affourtit JP, Shockley KR, Wilpan RY, Abdi FA, Bhardwaj S, Rollins J, Churchill GA, Paigen B.
Applying gene expression, proteomics and single-nucleotide polymorphism analysis for complex trait gene identification
Genetics. 2008 Mar;178(3):1795-805. PMCID: PMC2278051 [ Full Text ]

Individual Variation Microarray Experiment : 12 C57BL/6J male mice

Vedell PT, Svenson KL, Churchill GA.
Stochastic Variation of Transcript Abundance in C57BL/6J mice
BMC Genomics. 2011 Mar 30;12(1):167. PMCID: PMC3082245 [ Full Text ]

Cross platform comparison: variability in measured gene expression levels associated with three types of microarray platforms

Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G.
A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms
J Biomol Tech. 2004 Dec;15(4):276-84. PMCID: PMC2291701. [ Full Text ]

Design of Three- and Four-Color Microarray Experiments

Woo Y, Krueger W, Kaur A, Churchill G.
Experimental design for three-color and four-color gene expression microarrays
Bioinformatics. 2005 Jun;21 Suppl 1:i459-67. [ Full Text ]

Coordinated expression domains in mammalian genomes

Woo YH, Walker M, Churchill GA.
Coordinated expression domains in Mammalian genomes
PLoS One. 2010 Aug 18;5(8). pii: e12158. PMCID: PMC2923606 [ Full Text ]

Affymetrix expression data used to estimate p-values in small microarray experiments

Yang H, Churchill G.
Estimating p-values in small microarray experiments
Bioinformatics. 2007 Jan 1;23(1):38-43. [ Full Text ]

Dynamic gene expression changes during sleep in Drosophila brain

Zimmerman JE, Rizzo W, Shockley KR, Raizen DM, Naidoo N, Mackiewicz M, Churchill GA, Pack AI.
Multiple mechanisms limit the duration of wakefulness in Drosophila brain
Physiol Genomics. 2006 Nov 27;27(3):337-50. [ Full Text ]