{% extends "base.html" %} {% block title %}GeneNetwork{% endblock %} {% block css %} {% endblock %} {% block search %}
GNQA Search
{% endblock %} {% block content %}
{{ flash_me() }} {%if anon_collections | length > 0%}

Import Anonymous Collections

There {%if anon_collections | length > 1%}are{%else%}is{%endif%} {{anon_collections | length}} anonymous collection{%if anon_collections | length > 1%}s{%endif%} associated with your current session. What do you wish to do?

If you choose to ignore this, the anonymous collections will be eventually deleted and lost.

{%endif%}

Advanced Commands

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:

  • POSITION=(chr1 25 30) finds genes, markers, or transcripts on chromosome 1 between 25 and 30 Mb.
  • MEAN=(15 16) in the Combined field finds highly expressed genes (15 to 16 log2 units)
  • RANGE=(1.5 2.5) in the Any field finds traits with values with a specified fold-range (minimum = 1). Useful for finding "housekeeping genes" (1.0 1.2) or highly variable molecular assays (10 100).
  • LRS=(15 1000) or LOD=(2 8) finds all traits with peak LRS or LOD scores between lower and upper limits.
  • LRS=(9 999 Chr4 122 155) finds all traits on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.
  • cisLRS=(15 1000 5) or cisLOD=(2 8 5) finds all cis eQTLs with peak LRS or LOD scores between lower and upper limits, with an inclusion zone of 5 Mb around the parent gene.
  • transLRS=(15 1000 5) or transLOD=(2 8 5) finds all trans eQTLs with peak LRS or LOD scores between lower and upper limits, with an exclusion zone of 5 Mb around the parent gene. You can also add a fourth term specifying which chromosome you want the transLRS to be on (for example transLRS=(15 1000 5 7) would find all trans eQTLs with peak LRS on chromosome 7 that is also a trans eQTL with exclusionary zone of 5Mb).
  • POSITION=(Chr4 122 130) cisLRS=(9 999 10) 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.
  • RIF=mitochondrial searches RNA databases for GeneRIF links.
  • WIKI=nicotine searches GeneWiki for genes that you or other users have annotated with the word nicotine.
  • GO:0045202 searches for synapse-associated genes listed in the Gene Ontology.
  • RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10) finds diabetes-associated transcripts with peak trans eQTLs on Chr 2 between 100 and 105 Mb with LRS scores between 9 and 999.

Tutorials

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