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