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Data Set Group2: UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq modify this page

Data Set: UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq Log2 Z-score modify this page
GN Accession: GN813
GEO Series: No Geo series yet
Title: Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice
Organism: Mouse (Mus musculus, mm10)
Group: CFW
Tissue: Prefrontal Cortex mRNA
Dataset Status: Public
Platforms: Illumina ScriptSeq RNA-Seq v2
Normalization: RNA-seq
Contact Information
Abraham Palmer
University of California, San Diego
9500 Gilman Drive #0667
La Jolla, CA 92093 USA
Tel. 858-534-2093
Download datasets and supplementary data files

Specifics of this Data Set:

RNA-Seq Log2 Z-score

In general, the array data that we put in GeneNetwork has been logged and then z normalized, but instead of leaving the mean at 0 and the standard deviation of 1 unit, we shift up to a mean of 8 units and increase the spread by having an standard deviation of 2 units (what we call 2Z + 8 normalized data).  This removes negative values from the tables.


Although mice are the most widely used mammalian model organism, genetic studies have suffered from limited mapping resolution due to extensive linkage disequilibrium (LD) that is characteristic of crosses among inbred strains. Carworth Farms White (CFW) mice are a commercially available outbred mouse population that exhibit rapid LD decay in comparison to other available mouse populations. We performed a genome-wide association study (GWAS) of behavioral, physiological and gene expression phenotypes using 1,200 male CFW mice. We used genotyping by sequencing (GBS) to obtain genotypes at 92,734 SNPs. We also measured gene expression using RNA sequencing in three brain regions. Our study identified numerous behavioral, physiological and expression quantitative trait loci (QTLs). We integrated the behavioral QTL and eQTL results to implicate specific genes, including Azi2 in sensitivity to methamphetamine and Zmynd11 in anxiety-like behavior. The combination of CFW mice, GBS and RNA sequencing constitutes a powerful approach to GWAS in mice. Full article available here.

About the cases used to generate this set of data:

Phenotype, genotype and RNA-seq gene expression data is available at


About the tissue used to generate this set of data:

About the array platform:

About data values and data processing:

FPKM data were quantitle normalized for each ENSEMBL gene (mRNA) model (Identifiers such as ENSMUSG00000093778). Every gene/mRNA therefore has a mean expression value of 0 and a perfectly normal distribution, even if the original distribution was bimodal. The QQ plots is GN will be straight lines. There is no data at all on expression level in this original data set downloaded from http://dx.doi.org/10.5061/dryad.2rs41


Experiment Type:


A.A.P. conceived the study. C.C.P. and A.A.P. supervised the project. S.G. and P.C. designed and implemented the statistical and bioinformatics analyses with contributions from C.C.P., J.K.P. and A.A.P. N.M.G. designed and executed the RNA-seq and GBS protocols with assistance from E.A. and J.D. C.C.P. performed the behavioral phenotyping with assistance from E.L. and Y.J.P. A.L. performed the muscle and bone phenotyping with input from D.A.B. C.L.A.-B. performed the BMD phenotyping. C.C.P., S.G., P.C. and A.A.P. wrote the manuscript, with input from all co-authors.


Data source acknowledgment:

The authors wish to acknowledge technical assistance from: D. Godfrey, S. Lionikaite, V. Lionikaite, A.S. Lionikiene and J. Zekos as well as technical and intellectual input from M. Abney, J. Borevitz, K. Broman, N. Cai, R. Cheng, N. Cox, R. Davies, J. Flint, L. Goodstadt, P. Grabowski, B. Harr, E. Leffler, R. Mott, J. Nicod, J. Novembre, A. Price, M. Stephens, D. Weeks and X. Zhou. This project was funded by NIH R01GM097737 and P50DA037844 (A.A.P.), NIH T32DA07255 (C.C.P.), NIH T32GM07197 (N.M.G.), NIH R01AR056280 (D.A.B.), NIH R01AR060234 (C.L.A.-B.), the Fellowship from the Human Frontiers Science Program (P.C.) and the Howard Hughes Medical Institute (J.K.P.).

Study Id:

CITG Web services initiated January, 1994 as Portable Dictionary of the Mouse Genome; June 15, 2001 as WebQTL; and Jan 5, 2005 as GeneNetwork. This site is currently operated by Rob Williams, Pjotr Prins, Zachary Sloan, Arthur Centeno. Design and code by Pjotr Prins, Zach Sloan, Arthur Centeno, Danny Arends, Christian Fischer, Sam Ockman, Lei Yan, Xiaodong Zhou, Christian Fernandez, Ning Liu, Rudi Alberts, Elissa Chesler, Sujoy Roy, Evan G. Williams, Alexander G. Williams, Kenneth Manly, Jintao Wang, and Robert W. Williams, colleagues. Python Powered Registered with Nif
GeneNetwork support from:
  • The UT Center for Integrative and Translational Genomics
  • NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
  • NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
  • NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
  • NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
  • NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
  • NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)
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