From ea46f42ee640928b92947bfb204c41a482d80937 Mon Sep 17 00:00:00 2001 From: root Date: Tue, 8 May 2012 18:39:56 -0500 Subject: Add all the source codes into the github. --- web/dbdoc/BR_M2_1106_R.html | 2876 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 2876 insertions(+) create mode 100755 web/dbdoc/BR_M2_1106_R.html (limited to 'web/dbdoc/BR_M2_1106_R.html') diff --git a/web/dbdoc/BR_M2_1106_R.html b/web/dbdoc/BR_M2_1106_R.html new file mode 100755 index 00000000..05d714bc --- /dev/null +++ b/web/dbdoc/BR_M2_1106_R.html @@ -0,0 +1,2876 @@ + +UCHSC BXD Whole Brain M430 2.0 November 2006 RMA + + + + + + + + + + + + + + + + + +
+ + + +
+ + +

UCHSC BXD Whole Brain M430 2.0 November 2006 RMA + + modify this page

Accession number: GN123

+ +

+A +PhenoGen Informatics data set. Please cite: Saba L, Bhave SV, Grahame N, Bice P, Lapadat R, Belknap J, Hoffman PL, Tabakoff B (2006) Candidate genes and their regulatory elements: alcohol preference and tolerance. Mammalian Genome 17:669-688 Full Text PDF Version, Full Text HTML Version + +

+ + +

    Summary:

+ +

+This November 2006 data freeze provides estimates of mRNA expression in whole brains of BXD recombinant inbred strains and 20 common inbred strrains measured using Affymetrix MOE 430 v2 micorarrays. Data were generated at the University of Colorado at Denver and Health Science Center (UCDHSC) by Dr. Boris Tabakof and colleague. Single whole brain samples were hybridized to 248 individual arrays. Data were processed using the RMA protocol followed by a secondary quantile normalization at the probe set level and a scale and location adjustment to ensure an average expression level of 8 units and a standard deviation of 2 units for easy comparison to other transforms.

+ + +

The +PhenoGen Informatics web site provides additional analytic tools and transforms associated with these data. + +

+ +

    About the cases used to generate this set of data:

+ +

+This data set includes estimates of gene expression for 50 genetically uniform lines of mice: C57BL/6J (B6 or simply B), DBA/2J (D2 or D), 30 BXD recombinant inbred (RI) strain derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations, and 18 other inbred strains of mice available from the Jackson Laboratory. All mice used were naïve males from 70-90 days old. 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. Another 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.

+ +

In this mRNA expression database we generally used stock obtained directly from The Jackson Laboratory between 2003 and 2005.

+ +

    About the tissue used to generate these data:

+ +

+Naïve male mice were euthanized by CO2 exposure, and whole brains were removed and frozen on dry ice. Brains were stored at -70 deg C until used. The RNeasy Midi kit for lipid-rich tissues (Qiagen, Valencia, CA) was used to extract total RNA, and the RNeasy Mini kit (Qiagen) was used for cleanup. Biotin-labeled cRNA was obtained by in vitro transcription of the double-stranded cDNA that was originally synthesized from the total RNA. Each whole brain sample of biotin-labeled cRNA was fragmented and hybridized to a separate oligonucleotide array. After hybridization, the chips were stained with streptavidin-phycoerythrin conjugate and scanned using an Affymetrix GeneArray scanner. +

+ +

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BXD4060.30759.9945.5%4.2%50.4%1.370.76
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BXD4220.21692.3446.7%4.3%49.1%1.440.76
BXD4230.24984.5245.7%4.1%50.2%1.520.80
BXD4250.23685.2946.2%4.0%49.8%1.380.77
DBA/2J10.31379.6946.8%4.2%49.0%1.240.72
DBA/2J20.29482.2746.5%4.2%49.3%1.270.73
DBA/2J30.34978.5847.8%4.3%47.8%1.310.73
DBA/2J40.38972.0248.0%4.3%47.7%1.210.77
DBA/2J50.36266.7346.5%4.4%49.1%1.230.75
DBA/2J60.34179.8846.7%4.0%49.4%1.330.74
C57BL/6J10.29482.8446.7%4.1%49.2%1.230.76
C57BL/6J20.24280.4043.1%4.1%52.8%1.290.76
C57BL/6J30.250110.9047.8%4.0%48.2%1.320.76
C57BL/6J40.289101.8847.5%4.1%48.4%1.180.75
C57BL/6J50.299114.5948.7%4.1%47.3%1.130.74
C57BL/6J60.251105.9045.8%3.8%50.4%1.300.76
129P3/J10.49659.2641.9%3.5%54.5%1.280.79
129P3/J20.55050.8342.0%3.7%54.3%1.160.78
129P3/J30.44356.0843.0%3.8%53.3%1.220.73
129P3/J40.52158.9244.8%3.8%51.4%1.300.74
129P3/J50.50358.2644.9%3.8%51.3%1.320.74
129S1/SvImJ10.31166.7647.8%3.9%48.3%2.040.97
129S1/SvImJ20.26257.6344.5%3.9%51.6%1.610.81
129S1/SvImJ30.32262.6745.3%3.8%50.9%1.700.83
129S1/SvImJ40.185119.0250.2%4.4%45.5%1.660.75
A/J10.45351.8542.6%3.6%53.8%1.200.73
A/J20.39656.6145.9%3.9%50.2%1.210.76
A/J30.42162.3447.0%4.1%48.8%1.290.72
A/J40.50861.5248.2%4.1%47.7%1.220.74
AKR/J10.33154.7041.7%3.9%54.4%1.220.74
AKR/J20.46455.4644.1%3.7%52.1%1.300.76
AKR/J40.44453.6247.6%4.0%48.4%1.230.71
AKR/J50.43958.6247.4%4.3%48.3%1.230.70
BALB/cByJ10.33675.4950.0%4.1%45.9%1.540.82
BALB/cByJ20.28067.9347.1%4.3%48.7%1.430.76
BALB/cByJ30.31273.7747.7%4.1%48.2%1.790.92
BALB/cByJ40.26279.9746.1%4.1%49.8%1.380.79
BALB/cByJ50.27681.3246.3%4.1%49.6%1.340.79
BALB/cJ10.59154.2543.2%3.5%53.3%1.150.80
BALB/cJ20.34650.3639.9%3.3%56.8%1.200.77
BALB/cJ30.33352.7940.4%3.7%55.9%1.250.77
BALB/cJ50.49554.7845.0%3.7%51.3%1.150.72
BTBR T+tf/J30.31562.8346.4%4.1%49.5%1.380.78
BTBR T+tf/J40.24390.1251.6%4.8%43.6%1.310.75
BTBR T+tf/J50.29471.2146.6%4.3%49.0%1.410.77
BTBR T+tf/J60.26867.5346.6%4.2%49.2%1.320.75
BTBR T+tf/J10.37055.4045.7%4.1%50.2%1.410.75
BTBR T+tf/J20.48850.8947.2%4.2%48.6%1.360.75
C3H/HeJ10.51159.2043.3%3.4%53.3%1.170.83
C3H/HeJ20.40579.4941.3%3.3%55.5%1.180.83
C3H/HeJ30.45459.4741.7%3.5%54.9%1.160.81
C3H/HeJ40.44856.2841.5%3.5%55.0%1.160.79
C3H/HeJ50.38950.1741.1%3.6%55.2%1.240.79
C58/J10.33656.6646.0%4.2%49.8%1.290.73
C58/J20.37258.6146.7%4.3%49.0%1.210.71
C58/J30.36664.5846.8%4.2%49.0%1.200.72
C58/J40.37152.7245.3%4.1%50.6%1.240.72
CAST/EiJ10.46755.7447.1%3.8%49.1%1.390.79
CAST/EiJ20.54550.2946.8%3.8%49.4%1.340.84
CAST/EiJ30.46955.0847.4%4.0%48.5%1.320.76
CAST/EiJ40.39083.0553.0%4.4%42.6%1.360.72
CBA/J10.29267.2544.9%4.0%51.2%1.220.76
CBA/J20.34761.9946.4%4.0%49.7%1.250.82
CBA/J30.30562.1646.3%4.3%49.4%1.310.75
CBA/J40.30364.8246.5%4.0%49.5%1.340.76
CBA/J50.31364.1545.3%4.1%50.7%1.370.78
CBA/J60.36556.8445.6%4.1%50.4%1.310.76
FVB/NJ10.49763.9944.2%3.5%52.3%1.330.79
FVB/NJ20.47555.2444.8%3.8%51.4%1.330.74
FVB/NJ30.52756.0742.6%3.5%53.9%1.310.86
FVB/NJ40.44762.5641.7%3.5%54.8%1.240.82
KK/HIJ10.30993.5449.6%4.3%46.1%1.570.74
KK/HIJ20.29863.2448.0%4.4%47.6%1.370.72
KK/HIJ40.22393.0344.7%4.0%51.3%1.390.74
KK/HIJ50.153136.6751.9%4.6%43.5%1.240.71
MOLF/EiJ10.33967.1149.1%4.3%46.6%1.550.83
MOLF/EiJ20.31980.7349.1%4.2%46.7%1.520.78
MOLF/EiJ30.38069.0349.1%4.2%46.7%1.290.82
MOLF/EiJ40.23895.1948.7%4.1%47.2%1.350.79
NOD/LtJ10.35678.4249.1%4.2%46.7%1.350.76
NOD/LtJ20.42259.7147.4%4.0%48.5%1.250.73
NOD/LtJ30.37777.8449.8%4.0%46.2%1.240.75
NOD/LtJ40.53560.8650.6%4.4%45.0%1.280.74
NOD/LtJ50.33674.5846.6%3.9%49.5%1.320.72
NZW/LacJ20.44250.3144.6%4.1%51.3%1.330.82
NZW/LacJ30.33156.8644.2%4.0%51.7%1.600.78
NZW/LacJ40.33855.2344.1%4.0%51.9%1.310.78
NZW/LacJ50.35156.9049.3%4.3%46.5%1.300.75
PWD/PhJ10.44457.6547.2%3.9%48.9%1.620.78
PWD/PhJ20.32867.5847.3%4.2%48.5%1.360.76
PWD/PhJ30.32273.9047.5%4.0%48.5%1.460.81
PWD/PhJ40.27175.7946.1%4.0%50.0%1.390.79
PWD/PhJ50.191144.7357.7%5.0%37.3%1.360.67
SJL/J10.52854.5841.1%3.4%55.4%1.160.80
SJL/J30.66356.2141.8%3.3%55.0%1.220.75
SJL/J40.64652.9640.5%3.2%56.3%1.130.81
SJL/J50.63961.9144.8%3.4%51.9%1.370.79

+
+ +

    About the array platform:

+ +

+Affymetrix MOE430v2 GeneChip: The expression data were generated using 248 MOE430v2 arrays. The chromosomal locations of MOE430v2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6). This BLAT analysis is performed periodically 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 link in the Trait Data and Editing Form (right side of the Location line). +

+ + +

    About data processing:

+

+Probe set data: The expression data were processed by Laura Saba (UCDHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed within the rma function in R. This data set includes further normalization to produce final estimates of expression that can be compared directly to the other transforms.

+ + +

This includes an initial quantile normalization on the RMA normalized probe set data followed by a transformation to force an array average of 8 units and stabilized standard deviation of 2 units within each array. Please see Bolstad and colleagues (2003) for a helpful comparison of RMA and two other methods of processing Affymetrix array data sets. +

+ +

Expression estimates (strain averages) range from a low of about 3.8 for probe set 1457109_x_at to a high of 15 for Gapdh (probe set 1418625_s_at). The mean expression of 8.0 actually represents a relatively low value of expression (roughly 250 on the original scale) because it is the average of all transcripts on the array, including those that are not expressed. Nonetheless, it is possible to obtain good signal down to very low values. For example, probe set 1437432_a_at (Trim12) has an average expression of 4.56 (extremely low), but it still is associated with a strong QTL (LRS of 45) precisely at the location of the parent gene (Chr 7 at 104 Mb). This demonstrates unequivocally that the small strain differences in expression of Trim12 measured by probe set 1437432_a_at is not noise but is generated by true allelic differences in Trim12 mRNA binding to the arrays. + +

    Data source acknowledgment:

+

Data was generated with funds from NIAAA for Gene Array Technology Center (AA013162) and from the NIAAA Integrated Neuroinformatics Resource for Alcoholism (AA013524).

+ +

    Information about this text file:

+

This text file originally generated by RWW, YHQ, August for UTHSC Brain mRNA U74Av2 (Aug05) RMA. Updated for UC Denver Whole Brain M430v2 BXD (Nov06) RMA Data by LMS, November 2006. Updated by RWW, Feb 2008. +

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