diff options
| -rwxr-xr-x | wqflask/wqflask/templates/index_page_orig.html | 26 |
1 files 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 |