U74Av2 SScore April 05 / WebQTL

UTHSC Brain mRNA U74Av2 (Apr05) SScore modify this page

Accession number: GN63


This April 05 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n = 3) to 100 arrays. Data were processed using the S-score software of Zhang et al. 2002 and Kerns et al. 2003. The S- score method centers expression of every probe set at 0. The signal values are therefore strain deviations in Z score units from the grand mean based on all arrays.

    About the cases used to generate this set of data:

This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.

BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).

In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.

The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
8 Wks
20 Wks
52 Wks
8 Wks
20 Wks
52 Wks
C57BL/6J (B6) DBA/2J (D2)
B6D2F1 (F1) BXD1
BXD42 BXD67 (F8)
BXD68 (F9)

    How to download these data:

All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.

     About the samples used to generate these data:

Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.

     About the array platform:

Affymetrix U74Av2 GeneChip Annotation: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify UCSC and Verify Emsembllinks in the Trait Data and Editing Form (see buttons to the right side of the Location line). You can download the original BLAT output file that we have generated for the U74Av2 platform. The GeneNetwork includes a filtered subset of these data.

Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match (PM) probes and 16 mismatch controls (MM). Each set of these probe has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:

  • f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
  • s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
  • g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
  • r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
  • i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
  • st (sense target) : Designates a sense target; almost always generated in error.
  • Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.

        About data processing:

    Probe set data: The expression data were processed by RWW and Yanhua Qu at UTHSC to generate MAS 5 CEL files. These were then analyzed using the S-score algorithm (Zhang et al., 2002; Kerns et al., 2003) by Robnet Kerns and Michael Miles (Virginia Commonwealth University). The original CEL files produced by the Affymetrix analysis software were normalized for whole chip intensity and read into a version of the S-score software that produces an averaged CEL file across all arrays. This aveCEL was then used as the denominator to produce S-scores by pairwise analysis of all arrays. Probe set data are averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. This data set does not include further normalization.

    Regarding the S-score (from the Miles Lab web site): "The significance-score algorithm (S-score) was developed in our laboratory by Dr. Li Zhang. This produces a score for a comparison of the expression of a gene between two samples (e.g. control and "treated"). The S-score produces a robust measure of expression changes by weighting oligonucleotide pairs according to their signal strength above empirically determined noise levels. The procedure produces scores centered around "0" (no change) with a standard deviation of 1. Thus, scores >2 or <-2 from a single comparison have, on average, a 95% chance of being "real changes" in terms of the chip hybridization. This does not, however, imply that they are biologically reproducible."

         Data source acknowledgment:

    Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.

        Information about this text file:

    This text file originally generated by RWW, KFM, and Mike Miles, April 14, 2005. Updated by RWW, April 15, 2005.