Download - WebQTL
WebQTLWebQTL
Complex trait analysis beyond QTL mapping
www.webqtl.org webqtl.org
WebQTL AnalysisWebQTL Analysis
WebQTL ComponentsWebQTL Components
WebQTL pages
(Python)
WebQTL pages
(Python)
QTL mapping &Correlation
(C)
QTL mapping &Correlation
(C)
Phenotype &Genotype data
(MySQL)
Phenotype &Genotype data
(MySQL)
Search BXD trait dataSearch BXD trait data
Search resultsSearch results
Analysis selection windowAnalysis selection window
Genome-wide QTL mappingGenome-wide QTL mapping
Analysis selection windowAnalysis selection window
Correlation search resultsCorrelation search results
Multiple probe choiceMultiple probe choice
Mutiple probe: single chromosomeMutiple probe: single chromosome
TutorialTutorial
Choice is goodChoice is good
Stein, L (2002) Creating a bioinformatics nation. Nature 417, 119-20.
Trait data retrievalTrait data retrieval
cmd=get&probeset=101741_at&db=1&probe=all&format=col
Trait data formatted in rowsTrait data formatted in rows
cmd=get&probeset=101741_at&db=1&probe=all&format=row
Genotype data in columnsGenotype data in columns
cmd=geno&riset=BXD&chr=1&format=col
Single marker QTL mappingSingle marker QTL mapping
cmd=map&probeset=99856_r_at&db=1&sort=lrs&return=20
Peak LRS from interval mappingPeak LRS from interval mapping
cmd=interval&probeset=99856_r_at&db=1&sort=pos&return=10
Scripted mapping and data retrievalScripted mapping and data retrieval
PM probe p-values
0.0
0.2
0.4
0.6
0.8
1.0
0 5000 10000 15000
Rank of sorted p-value
p-v
alu
e
PM probe p-values
0.0
0.2
0.4
0.6
0.8
1.0
0 5000 10000 15000
Rank of sorted p-value
p-v
alu
e
PM probe p-values
0.000
0.002
0.004
0.006
0.008
0.010
0.012
0.014
0.016
0.018
0.020
0 50 100 150 200 250 300
Rank of sorted p-value
p-v
alu
e
PM probe p-values
0.000
0.002
0.004
0.006
0.008
0.010
0.012
0.014
0.016
0.018
0.020
0 50 100 150 200 250 300
Rank of sorted p-value
p-v
alu
e
What WebQTL is notWhat WebQTL is not
• P-value plot of every 10th from 195,327 values
Detail
AcknowledgementsAcknowledgements
• Web site design & coding– Jintao Wang– Kenneth F Manly– Alex G Williams
• Published phenotype data– Elissa S Chesler– John C Crabbe– John K Belknap– Byron Jones– Ryan McNieve– Nathan Copeland
• Genotype/Genomic data– Lu Lu– Jing Gu– Shuhua Qi– John Hogenesch– Timothy Wiltshire– Yanhua Qu
• Brain expression data– Lu Lu– Siming Shou– Yanhua Qu– John Mountz– HuiChen Su– David Threadgill
• HSC expression data– Gerald de Haan– Michael Cooke– Leonid Bystrykh– Ellen Weersing– Bert Dontje– Andrew Su
• Cerebellum expression data– UTHSC-St Jude Cerebellum Consortium
• Vision and Motivation– Robert W Williams