GeneNetwork GeneNetwork 2
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Select and Search
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.
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GeneNetwork 2
Main website
at UTHSC
Backup
instance of GN2
GeneNetwork v1
Main website
at UTHSC
Affiliates
GeneNetwork 1
at UTHSC
Systems Genetics
at EPFL
Bayesian Network Web Server
at UTHSC
GeneWeaver
PhenoGen
at University of Colorado
WebGestalt
at Baylor
GeneNetwork hosted portals
Omics Portal For Addiction Research
GN4MSK musculoskeletal
GeneCup: Mining PubMed for Gene Relationships using Custom Ontologies