src/hg/makeDb/trackDb/nci60.html 1.4

Index: src/hg/makeDb/trackDb/nci60.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/nci60.html,v
retrieving revision 1.3
retrieving revision 1.4
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 <h2>Description</h2>
 
 <p>Expression <a href="http://genome-www.stanford.edu/nci60/" 
 TARGET=_BLANK>data</A> from "Systematic variation in gene expression 
 patterns in human cancer cell lines"  
 <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=10700174&amp;dopt=Abstract" 
 TARGET=_BLANK>[pubmed]</a>, Ross et al., <EM>Nature Genetics</EM> 2000 Mar; 24(3):227-35. 
 cDNA microarrays were
 used to explore the variation in expression of approximately 8,000
 unique genes among the 60 cell lines used in the National Cancer
 Institute's screen for anti-cancer drugs. The authors have provided a
 <a href="http://genome-www.stanford.edu/nci60/supplement.shtml" 
 TARGET=_BLANK>web supplement </a>
 where more data and experimental description can be obtained. cDNA
 probes were placed on the draft human genome using genebank sequences
-referenced by the <a href="http://image.llnl.gov/" 
+referenced by the <a href="http://image.hudsonalpha.org/"
 TARGET=_BLANK>IMAGE</a> clone ids. 
 
 <p>The data are shown in a tabular format in which each column of
 colored boxes represents the variation in transcript levels for a
 given cDNA across all of the array experiments, and each row
 represents the measured transcript levels for all genes in a single
 sample. The variation in transcript levels for each gene is
 represented by a color scale, in which red indicates an increase in
 transcript levels, and green indicates a decrease in transcript
 levels, relative to the reference sample. The saturation of the color
 corresponds to the magnitude of transcript variation. A black color
 indicates an undetectable change in expression, while a gray box
 indicates missing data.
 
 <h2>Display Options</h2>
 This track has filter options to customize tissue types presented and
 the color of the display.
 
 <p><b>Combine Arrays: </b> This option is only valid when the track is 
 displayed in full. It determines how the experiments are displayed. The
 options are:
 <ul>
 <li><b>Arrays Grouped by Tissue Median: </b> <i>(default)</i> Displays the median of the log ratio scores of all cell lines 
 from the different tissue types.</li>
 <li><b>Arrays Grouped by Tissue Mean: </b> Displays the mean of the log ratio scores of all cell lines 
 from the different tissue types.</li>
 <li><b>All Arrays (experiments): </b> Displays the log ratio score for all cell line experiments.
 </li>
 </ul>
 <b>Color Scheme: </b> 
 Data are presented using two color false display. By default
 the Brown/Botstein colors of red -> positive log ratio, green -> negative log ratio are used.
 However, a yellow/blue option can be selected for those who are colorblind.
 
 <h2>Details Page</h2> 
 On the details page, the probes presented
 correspond to those contained in the window range displayed on the Genome
 Browser. The exon probe and experiment selected are highlighted in
 blue.