583e30e3cbfc3c95eb94696d51c8979493caa9a3 galt Mon May 20 23:49:34 2019 -0700 html pages fixed for problems found with htmlCheck validate and strictTagNestCheck diff --git src/hg/near/hgNear/hgNearData/affyExonTissuesGsDistance.html src/hg/near/hgNear/hgNearData/affyExonTissuesGsDistance.html index 6bcf3d5..7fe8913 100644 --- src/hg/near/hgNear/hgNearData/affyExonTissuesGsDistance.html +++ src/hg/near/hgNear/hgNearData/affyExonTissuesGsDistance.html @@ -1,54 +1,54 @@ <H3>Description</H3> <P> This column shows the similarity of the expression (distance) from the Affymetrix All Exon dataset of each gene to the selected gene. Genes with identical expression profiles show a value of zero. This column shows data only for the 1000 genes (including splicing variants) that have the most similar expression profiles. </P> <H3>Methods</H3> <P> RNA (from a commercial source) from 11 tissues was hybridized to Affymetrix All Exon 1.0 ST arrays. For each tissue, 3 replicate experiments were done for a total of 33 arrays. The arrays' raw signal intensity was normalized with a quantile normalization method, then run through the PLIER algorithm. The normalized data were then converted to log-ratios, which are displayed as green for negative log-ratios (under-expression), and red for positive (over-expression).</P> <P>When calculating expression ratios, the overall expression level in the denominator was calculated by first taking the median of replicates for each tissue and then taking the median of these medians. </P> <P> To associate particular genes with expression data, the following algorithm was used: for each gene, the overlapping exons from the microarray dataset were collected and the median intensity of these was assigned to the gene. If the gene contained exons not overlapping an exon from the microarray, those exons were ignored. If the microarray dataset contained exons not overlapping a gene, those were ignored as well. Once the overall expression level of each gene was determined, the log-ratio was calculated. In addition, the median was taken for replicate arrays per tissue for both the absolute -and log-ratio varieties.</P. +and log-ratio varieties.</P> <P> The expression distance between two genes is a weighted sum computed with the following formula: <PRE> delta(a,b) = sum(w[i] * |a[i] - b[i]| ) / sum(w[i]) </PRE> where <em>a</em> and <em>b</em> are expression vectors associated with the two genes indexed by a microarray, <em>w</em> is an array of weights, and the sums are taken over all microarray. Each microarray is weighted equally in this case, because all tissues have three replicates. </P> <H2>Credits</H2> <P> The data for this track were provided and analyzed by <A HREF="http://www.affymetrix.com/" TARGET=_blank>Affymetrix</A>. </P> <H2>Links</H2> <P><UL><LI> <A HREF="http://www.affymetrix.com/products/arrays/specific/exon.affx" TARGET=_blank>AffyMetrix Human Exon 1.0 ST array web page</A></LI> <LI><A HREF="http://www.affymetrix.com/support/technical/sample_data/exon_array_data.affx" TARGET=_blank>AffyMetrix Human Exon data</A></LI> <LI><A HREF="http://www.affymetrix.com/support/technical/technotes/plier_technote.pdf" TARGET=_blank>PLIER algorithm documentation (PDF).</A></LI></UL></P>