ComparaGRID
Andy Law
eScience Grant-holders’ workshop
November 2004
Collaborators

Roslin Institute

EBI

Institute for Food Research

John Innes Centre

Manchester

Newcastle University (Maths & Stats)

Newcastle University (Computing Science)

SCRI
Genomics and Bioinformatics
Aim

To develop ‘enabling technologies’
for comparative genomics
Genomics and Bioinformatics
Why?

… an example …
Genomics and Bioinformatics
Identification of QTL

What is the actual gene controlling the trait?
Comparative genomics

A tool to help?
Genomics and Bioinformatics
Identification of QTL gene
Species A
QTL
is in here
somewhere
{
Species B
A
A
B
B
C
C
D
D
E
E
Genomics and Bioinformatics
Identification of QTL gene
Species A
QTL
is in here
somewhere
{
A
Species B
A
Gene 1
Gene 2
B
B
C
C
D
D
E
E
Gene 3
}
Gene 4
These are
potential
candidate
genes
Genomics and Bioinformatics
Pig Fat QTL
Genomics and Bioinformatics
Linkage and RH maps
Fat
Trait
location
Linkage
Map
Radiation
Hybrid Map
Genomics and Bioinformatics
Human homology
Pig
Fat
Trait
location
Linkage
Map
Radiation
Hybrid Map
Cytogenetic
Map
Genomics and Bioinformatics
Physical clones
Pig
Human
BAC1
BAC2
Fat
BAC3
Trait
location
Linkage
Map
Radiation
Hybrid Map
Cytogenetic
Map
Physical
Mapping
Genomics and Bioinformatics
Chicken EST homologues
Pig
Chicken
Human
BAC1
EST1
BAC2
Fat
EST2
BAC3
Trait
location
Linkage
Map
Radiation
Hybrid Map
Cytogenetic
Map
Physical
Mapping
Genomics and Bioinformatics
Expression data
Pig
Chicken
Human
BAC1
EST1
BAC2
Fat
EST2
BAC3
Trait
location
Linkage
Map
Radiation
Hybrid Map
Cytogenetic
Map
Physical
Mapping
Expression
Analysis
Genomics and Bioinformatics
Supporting literature
Pig
Chicken
Human
BAC1
EST1
BAC2
Fat
EST2
BAC3
Trait
location
Linkage
Map
Radiation
Hybrid Map
Linked
References
Cytogenetic
Map
Physical
Mapping
Expression
Analysis
Genomics and Bioinformatics
Problem

We can compute this, computers
can’t
Genomics and Bioinformatics
Making the links

Define a vocabulary that describes
links


A ‘is an alias of’ B
C ‘is contained by’ D
• Ergo D ‘contains’ C



E ‘is homologous/orthologous to’ F
G ‘differs from’ G1
… etc. …
Genomics and Bioinformatics
Storing/presenting the links

Links are data too…

Assertions of identity, similarity etc.
should be treated in exactly the
same way as a gene sequence or a
spot on a micro-array
Genomics and Bioinformatics
Ideal outcomes

An ontology of comparative genomics
relationships

An infrastructure for rapidly generating
genome-to-genome comparisons

Applications that utilise these to generate
problem-focussed hypotheses
Genomics and Bioinformatics
Making the links

Different name, same thing…

TGF-B1, TGFB1, Tgfb1, Transforming
Growth Factor Beta 1, TGF 1

TGF-B1, TGF-B4, TGF-B5
Genomics and Bioinformatics
Making the links

Same name, different thing…

There are at least 6 different markers
recorded as ‘GH’ within ARKdb-pig

Some primer pairs amplify multiple loci
and the same anonymous symbol has
thus been assigned to multiple
chromosomal locations
Genomics and Bioinformatics
Making the links

Gene families

TGF-B1, TGF-B2, TGF-B3, TGF-B4, TGFB5

Chicken, human have 3, Xenopus has 2
Genomics and Bioinformatics
Making the links

Fat QTLs


Abdominal fat pad, shoulder, back,
interstitial (marbling)
Other phenotypes


Are chicken wings equivalent to arms
or limbs in general?
What about drosophila wings?
Genomics and Bioinformatics