WebQTL
 
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Overview modify this page

GeneNetwork (GN) provides a scriptable interface that allows other services and web users to retrieve data, map QTLs, generate lists of covariates, or to link to the most appropriate page of data for a particular tissue or transcript. This page documents the GN scriptable interface. GN functions are invoked using commands, which usually takes the form of a URL beginning
http://robot.genenetwork.org/webqtl/main.py?...
At the end of this type of command, after the question mark, you need to add a set of keywords and values separated by the = character, for example, cmd=get or probeset=100011_at. Keywords and values that GN will recognize are listed and explained in the table below.
The keyword-value pairs should be separated by the & character. A complete query might look like
cmd=get&probeset=100011_at&probe=all&format=column
The order of the keyword-value pairs in the list is unimportant. However, the cmd keyword is required and its value determines what other keywords are required or allowed. In examples, we always use the cmd keyword first.
Putting the whole query together results in a string that looks like http://robot.genenetwork.org/webqtl/main.py?cmd=get&probeset=100011_at&probe=all&format=column
Although this command is shown on two lines of text, it is really just one line, and there should be no carriage return or line break.

Specific commands

cmd=genotype retrieves genotype data for any of the supported sets of recombinant inbred lines.
cmd=get or cmd=trait retrieves trait data from databases of published phenotypes or gene expression data. It can also retrieve marker genotypes as numerical codes for correlation searches.
cmd=map retrieves trait data and searches for associations among BXD marker genotypes, returning marker names, regression coefficients and likelihood ratio statistics.
cmd=interval retrieves trait data and performs interval mappng, returning map positions of peak likelihood ratio statistic.
cmd=correlation retrieves trait data and searches for correlations with traits in another (or the same) trait database. cmd=correlation and cmd=pearson use Pearson product-moment correlation. cmd=spearman uses Spearman rank-sum correlation.

Commands and Keywords

Function Command
keyword-value
Other keywords
(bold keywords are required)
Allowed values
[Comments or descriptions in square brackets]
Retrieve genotype data cmd=genotype
cmd=gen
riset axb, bxa, bxd, bxh, cxb
    chr (3) 1, 2, 3, ..., 19, X
    format (4) row, column
Example: http://robot.genenetwork.org/webqtl/main.py?cmd=genotype&riset=BXD&chr=1&format=column
 
Retrieve trait data cmd=get
cmd=trait
cmd=tra
probeset (1) [Probe or probeset identifier, trait record number (for db=3), or marker name (for db=4)]
    db Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
    probe (1) all pm mm
OR
[Affymetrix cell location code] (3)
    format (4) row, column
Example: http://robot.genenetwork.org/webqtl/main.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&probe=119637&format=col
 
Single-marker regression cmd=map probeset (1) [Probe or probeset identifier, trait record number (for db=3) or marker name (for db=4)]
    db Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
    probe (1) all
[Affymetrix cell location code] (2)
    return number of LRS values to be reported; all LRS are reported if omitted
    sort lrs [sorts by descending pvalue]
[sorts by ascending position by default]
Example: http://robot.genenetwork.org/webqtl/main.py?cmd=map&probeset=98332_at&db=bra08-03MAS5&sort=lrs&return=20
 
QTL interval mapping cmd=interval
cmd=int
probeset (1) [Probe or probeset identifier, trait record number (for db=3), or marker name (for db=4)]
    db Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
    probe (1) [Affymetrix cell location code] (2)
    chr 1, 2, 3, ..., 19, X
    sort lrs [sorts by descending pvalue]
[sorts by ascending position by default]
Example: http://robot.genenetwork.org/webqtl/main.py?cmd=interval&probeset=98332_at&db=bra08-03MAS5&chr=1
 
Trait correlation search cmd=correlation
cmd=cor
cmd=pearson
cmd=pea
cmd=spearman
cmd=spe
probeset (1) [Affymetrix probeset identifier, trait record number (for db=3) or marker name (for db=4)]
    db Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
    searchdb Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
    probe (1) [Affymetrix cell location code] (2)
    return [Maximum number of correlations to be reported]
    sort

pvalue [sorts by ascending pvalue]
[sorts by descending correlation by default]

    id yes [Includes NCBI Entrez Gene ID for each transcript in the output (for expression data only).]
only [Returns only NCBI Entrez Gene ID for each transcript (for expression data only).]
Example: http://robot.genenetwork.org/webqtl/main.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDPublish&return=500&sort=pvalue
 
Open Trait Data and Analysis Form cmd=show
cmd=shw
probeset (1) [Affymetrix probeset identifier, trait record number (for db=3) or marker name (for db=4)]
    db Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
    probe (1) [Affymetrix cell location code] (2)
Example: http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db=HC_M2_0606_M&probeset=1415670_at&probe=269753
 
The script below is used to filter a list of probes or probe sets that target the same gene or transcript to find the single probe or probe set with highest expression and to then display the Statistics Page for that particular data. This script does not use the cgi-bin format.
Show Best Trait Data Statistics Page parameters
 
examples
 
Notes
  gene=
refseq=
geneid=
database=
searchAlias=
gene=Rho
refseq=NM_145383
geneid=212541
database=Eye_M2_0906_R
searchAlias=1
There are three supported search term types: 1. Gene symbol, 2. RefSeq identifier, 3. Entrez gene identifier. Although not recommended, the string "&searchAlias=1" can be added at the end of the command to retrieve data using the alias of a proper gene symbol when the original does not work. Thus "gene=RP4" will resolve to "gene=Rho" only if you add "&searchAlias=1" at the end of the command.
Each database stored in GN is assigned a short code required to identify the particular database from which you would like to retrieve data.
Example 1: http://gn1.genenetwork.org/webqtl/main.py?FormID=showBest&gene=Rho&database=HC_M2_0606_P
Example 2: http://gn1.genenetwork.org/webqtl/main.py?FormID=showBest&refseq=NM_145383&database=HC_M2_0606_P
Example 3: http://gn1.genenetwork.org/webqtl/main.py?FormID=showBest&geneid=212541&database=HC_M2_0606_P
Example 4: http://gn1.genenetwork.org/webqtl/main.py?FormID=showBest&gene=RP4&database=HC_M2_0606_P&searchAlias=1
This script was originally written to allow connections from the NEIBank to GeneNetwork by H. Li and R. Williams (see News of April 25, 2007).
 
Search for gene data cmd=search
cmd=sch
gene
refseq
genbankid
The name or ID of the gene or protein to be searched, choose one and only one type of identifier
    alias [0 or 1] Whether to search for possible aliases (only when a gene name is supplied), optional, disabled by default (0)
    species Optional, only human, mouse and rat are supported now. Default is mouse if not specified.
    tissue Optional, if not specified, display traits from all available tissues. For tissue abbreviations, please check http://gn1.genenetwork.org/webqtl/main.py?cmd=help&topic=tissue
    format [html or text], Optional, if not specified, return result in HTML format
Example 1 : http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene=ddx25
Example 2 : http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&refseq=NM_133594&species=rat
Example 3 : http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&genbankid=AW047046
Example 4 : http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene=GRTH&alias=1&species=rat&tissue=fat
Example 5 : http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene=Grin2b&tissue=hip&format=text
 

Notes

  1. A value is required for the probeset but not for probe keyword. With only probeset, commands will retrieve the average for the probeset from different average method. With probeset and probe=all, commands will retrieve data for all probes of that probeset; with probe, data for a single probe. If the specified probeset and probe are inconsistent, no data is returned.
  2. The Affymetrix cell location code is six characters. The first three characters are the column or x location, and the last three the row or y location; for example, 237198. If the column has less than three digits, it should be preceded by one or two X characters to make three characters. Similarly, the row should be prefixed with one or two Y characters, if necessary; for example, X24YY9 or XX8Y34.
  3. If chr is omitted, command will retrieve information for all chromosomes.
  4. If format is omitted, row formatting is the default.
CITG Web services initiated January, 1994 as Portable Dictionary of the Mouse Genome; June 15, 2001 as WebQTL; and Jan 5, 2005 as GeneNetwork.This site is currently operated by Rob Williams, Pjotr Prins, Zachary Sloan, Arthur Centeno. Design and code by Pjotr Prins, Zach Sloan, Arthur Centeno, Danny Arends, Christian Fischer, Sam Ockman, Lei Yan, Xiaodong Zhou, Christian Fernandez, Ning Liu, Rudi Alberts, Elissa Chesler, Sujoy Roy, Evan G. Williams, Alexander G. Williams, Kenneth Manly, Jintao Wang, and Robert W. Williams, colleagues. Python Powered Registered with Nif
GeneNetwork support from:
  • The UT Center for Integrative and Translational Genomics
  • NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
  • NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics,and the Addictome (P30 DA044223, 2017-2022)
  • NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
  • NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
  • NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
  • NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)