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<blockquote>
<p>This is a subtractive dataset. The Normal retina dataset was subtracted from the ONC data set probe by probe to create a data set of the changes occurring following ONC. This data set can be used to define gene changes following ONC. It is not compatible with most of the bioinformatic tools available on GeneNetwork.</p>
<p>HEI Retina Illumina V6.2 (April 2010) RankInv was normalized and scaled by William E. Orr and uploaded by Arthur Centeno and Xiaodong Zhou on April 7, 2010. This data set consists of either 69 BXD strains (Normal data set) or 75 BXD strains (Full data set), C57BL/6J, DBA/2J, both reciprocal F1s, and BALB/cByJ. A total of either 74 strains (Normal data set) or 80 strains (Full data set) were quantified.</p>
<p>COMMENT on FULL versus NORMAL data sets: For many general uses there is no significant difference between FULL and NORMAL data sets. However, the FULL data set includes strains with high endogenous Gfap mRNA expression, indicative of reactive gliosis. For that reason, and to compare to OPTIC NERVE CRUSH (ONC), we removed data from six strains to make the NORMAL data set.</p>
<p>The NORMAL data set exludes data from BXD24, BXD32, BXD49, BXD70, BXD83, and BXD89. BXD24 has known retinal degeneration and is now known officially as <a href="https://www.jax.org/strain/000031"> BXD24/TyJ-Cep290/J</a>, JAX Stock number 000031. BXD32 has mild retinal degeneration. The NORMAL data set does include BXD24a, now also known as BXD24/TyJ (JAX Stock number 005243).</p>
<p>The data are now open and available for analysis.</p>
<p><strong>Please cite</strong>: Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372. <a class="fs14" href="http://www.molvis.org/molvis/v17/a153/" target="_blank">Full Text PDF or HTML</a></p>
<p>This is rank invariant expression data that has been normalized using what we call a 2z+8 scale, but without special correction for batch effects. The data for each strains were computed as the mean of four samples per strain. Expression values on a log2 scale range from 6.25 to 18.08 (11.83 units), a nominal range of approximately 3600-fold. After taking the log2 of the original non-logged expression estimates, we convert data within an array to a z score. We then multiply the z score by 2. Finally, we add 8 units to ensure that no values are negative. The result is a scale with a mean of 8 units and a standard deviation of 2 units. A two-fold difference in expression is equivalent roughly to 1 unit on this scale.</p>
<p>The lowest level of expression is 6.254 for ILMN_2747167 (Arhgap11a) from HEI Retina Illumina V6.2 (April 2010) RankInv **. Lowest single data about 5.842.</p>
<p>The highest level of expression is 18.077 for ILMN_2516699 (Ubb). Highest single value is about 18.934.</p>
<p> </p>
</blockquote>
<p>Other Related Publications</p>
<blockquote>
<p> </p>
<ol>
<li>Geisert EE, Lu L, Freeman-Anderson NE, Templeton JP, Nassr M, Wang X, Gu W, Jiao Y, Williams RW.:Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice. Molecular Vision 2009 Aug 31;15:1730-63, (<a class="fs14" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736153/?tool=pubmed" target="_blank">Link</a>)</li>
<li>Geisert EE, Jr., Williams RW: The Mouse Eye Transcriptome: Cellular Signatures, Molecular Networks, and Candidate Genes for Human Disease. In Eye, Retina, and Visual System of the Mouse. Edited by Chalupa LM, Williams RW. Cambridge: The MIT Press; 2008:659-674</li>
<li>Peirce JL, Lu L, Gu J, Silver LM, Williams RW: A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 2004, 5:7. (<a class="fs14" href="http://www.biomedcentral.com/1471-2156/5/7" target="_blank">Link</a>)</li>
<li>Templeton JP, Nassr M, Vazquez-Chona F, Freeman-Anderson NE, Orr WE, Williams RW, Geisert EE: Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush. BMC Neurosci. 2009, July 30;10:90.(<a class="fs14" href="http://www.biomedcentral.com/1471-2202/10/90" target="_blank">Link</a>)
<p> </p>
<p> </p>
</li>
</ol>
</blockquote>
<blockquote><strong>Other Data Sets</strong> Users of these mouse retina data may also find the following complementary resources useful:
<ol>
<li><a class="fs14" href="http://neibank.nei.nih.gov/index.shtml" target="_blank">NEIBank</a> collection of ESTs and SAGE data.</li>
<li><a class="fs14" href="http://www.sph.uth.tmc.edu/Retnet/" target="_blank">RetNet</a>: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases</li>
<li><a class="fs14" href="http://cepko.med.harvard.edu/" target="_blank">Mouse Retina SAGE Library</a> from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.</li>
<li><a class="fs14" href="http://dro.hs.columbia.edu/" target="_blank">Digital reference of ophthalmology </a> from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.</li>
<li><a class="fs14" href="http://www.scripps.edu/cb/friedlander/gene_expression/search.html" target="_blank">Mouse Retinal Developmental Gene Expression</a> data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).</li>
<li><a class="fs14" href="http://microarray-pubs.stanford.edu/eyecompartments/" target="_blank">Data sets on differential gene expression in anatomical compartments of the human eye</a> from Pat Brown's lab. View expression signatures for different ocular tissues using the <strong>geneXplorer 2.0</strong>.</li>
</ol>
</blockquote>
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