From 31b4ef601e16f8e6d42986a0086864854b42461a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 13 Aug 2019 15:10:58 -0500
Subject: Updated text on main search page

---
 wqflask/wqflask/templates/index_page_orig.html | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index ed91a886..bdf51bf8 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -138,19 +138,32 @@
                         <h2>Advanced commands</h2>
                     </div>
 
-                    <p>You can also use advanced commands. Copy these simple examples into the Get Any or Combined search fields:</p>
+                    <p>You can also use advanced commands. Copy these simple examples into the Get Any field for single term searches and Combined for searches with multiple terms:</p>
 
                       <ul>
                         <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
                         chromosome 1 between 25 and 30 Mb.</li>
 
-                        <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
-                        highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L">LRS</a>
-                        linkage between 23 and 46.</li>
+                        <li><b>MEAN=(15 16)</b> in the <b>Combined</b> field finds
+                        highly expressed genes (15 to 16 log2 units)</li>
 
                         <li><b>RANGE=(1.5 2.5)</b> in the <b>Any</b> field finds traits with values with a specified fold-range (minimum = 1). 
                         Useful for finding "housekeeping genes" <b>(1.0 1.2)</b> or highly variable molecular assays <b>(10 100)</b>.</li>
 
+                        <li><b>LRS=(15 1000)</b> or <b>LOD=(2 8)</b> finds all traits with peak LRS or LOD scores between lower and upper limits.</li>
+
+                        <li><b>LRS=(9 999 Chr4 122 155)</b> finds all traits on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.</li>
+
+                        <li><b>cisLRS=(15 1000 5)</b> or <b>cisLOD=(2 8 5)</b> finds all cis eQTLs with peak LRS or LOD scores between lower and upper limits,
+                            with an <b>inclusion</b> zone of 5 Mb around the parent gene.</li>
+
+                        <li><b>transLRS=(15 1000 5)</b> or <b>transLOD=(2 8 5)</b> finds all trans eQTLs with peak LRS or LOD scores between lower and upper limits,
+                            with an <b>exclusion</b> zone of 5 Mb around the parent gene.</li>
+
+                        <li><b>POSITION=(Chr4 122 130) cisLRS=(9 999 10)</b>
+                            finds all traits on Chr 4 from 122 and 155 Mb with cisLRS scores
+                            between 9 and 999 and an inclusion zone of 10 Mb.</li>
+
                         <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF">
                         GeneRIF</a> links.</li>
 
@@ -162,11 +175,6 @@
                         <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202">
                             Gene Ontology</a>.</li>
 
-                        <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b>
-                        finds synapse-associated genes with <a href="http://www.genenetwork.org/glossary.html#E">
-                        cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores
-                        between 9 and 999.</li>
-
                         <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
                         finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E">
                         trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
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