emage
edinburgh mouse atlas of gene
expression
Jeff Christiansen PhD
Project Leader
EMAGE Database
emage edinburgh mouse atlas of gene expression
EMAGE - a novel bioinformatics resource
emage edinburgh mouse atlas of gene expression
APOPTOSIS
METABOLIC ACTIVITY
Acridine Orange
J. Burns
University of Bristol
Positron Emission Tomography
R. Coghill
Wake Forest University
CELL DIVISION
CELL LINEAGE
anti-BrdU staining
J. McDearmid
McGill University
Sigolène Meilhac
Institut Pasteur
TRANSGENICS
cre inducedLacZ expression
W. Hsu, University of Rochester
GENE EXPRESSION
Carol Wicking, IMB
emage edinburgh mouse atlas of gene expression
EMAGE
Aim to describe the expression patterns of genes in the
mouse during embryonic development as
detected by in situ methods
emage edinburgh mouse atlas of gene expression
EMAGE
Aim to describe the expression patterns of genes in the
mouse during embryonic development as
detected by in situ methods -
in situ hybridisation (detecting mRNA distribution)
immunohistochemistry (detecting protein distribution)
emage edinburgh mouse atlas of gene expression
EMAGE
Aim to describe the expression patterns of genes in the
mouse during embryonic development as
detected by in situ methods -
in situ hybridisation (detecting mRNA distribution)
immunohistochemistry (detecting protein distribution)
Develop tools for analysis of this data
emage edinburgh mouse atlas of gene expression
Wholemount samples
fixed whole embryo
emage edinburgh mouse atlas of gene expression
Wholemount samples
anti-sense
mRNA
probe to gene ‘X’
anti-‘protein X’
antibody
AAAAA
AAAAA
fixed whole embryo
Bind and then
detect gene
specific reagent
in situ
OR
emage edinburgh mouse atlas of gene expression
Wholemount samples
anti-sense
mRNA
probe to gene ‘X’
anti-‘protein X’
antibody
AAAAA
OR
AAAAA
Hybridise probe
fixed whole embryo
Bind and then
detect gene
specific reagent
in situ
stained whole embryo
emage edinburgh mouse atlas of gene expression
Sectioned samples
section
whole embryo
emage edinburgh mouse atlas of gene expression
Sectioned samples
section
whole embryo
emage edinburgh mouse atlas of gene expression
Sectioned samples
anti-sense
mRNA
probe to gene ‘X’
anti-‘protein X’
antibody
AAAAA
AAAAA
section
Bind and then
detect gene
specific reagent
to the section
whole embryo
OR
emage edinburgh mouse atlas of gene expression
Sectioned samples
anti-sense
mRNA
probe to gene ‘X’
anti-‘protein X’
antibody
AAAAA
OR
AAAAA
section
Bind and then
detect gene
specific reagent
to the section
whole embryo
stained section
emage edinburgh mouse atlas of gene expression
Text based approach
Fgf8
Patrick Tam
emage edinburgh mouse atlas of gene expression
Text based approach
Person 1:
isthmus
branchial arch
distal telencephalon
emage edinburgh mouse atlas of gene expression
Text based approach
Person 1:
isthmus
branchial arch
distal telencephalon
Person 2:
midbrain-hindbrain organiser
anterior 1st branchial arch
anterior forebrain
posterior 2nd branchial arch
emage edinburgh mouse atlas of gene expression
Text based approach
Person 1:
isthmus
branchial arch
distal telencephalon
Problems with using text:
Person 2:
midbrain-hindbrain organiser
anterior 1st branchial arch
anterior forebrain
posterior 2nd branchial arch
emage edinburgh mouse atlas of gene expression
Text based approach
Person 1:
isthmus
branchial arch
distal telencephalon
Person 2:
midbrain-hindbrain organiser
anterior 1st branchial arch
anterior forebrain
posterior 2nd branchial arch
Problems with using text:
Different people use different words
(therefore controlled vocabularies must be used)
emage edinburgh mouse atlas of gene expression
Text based approach
Person 1:
isthmus
branchial arch
distal telencephalon
Person 2:
midbrain-hindbrain organiser
anterior 1st branchial arch
anterior forebrain
posterior 2nd branchial arch
Problems with using text:
Different people use different words
(therefore controlled vocabularies must be used)
Anatomical structures may not be named (or the biologist doesn’t know it)
emage edinburgh mouse atlas of gene expression
Text based approach
Person 1:
isthmus
branchial arch
distal telencephalon
Person 2:
midbrain-hindbrain organiser
anterior 1st branchial arch
anterior forebrain
posterior 2nd branchial arch
Problems with using text:
Different people use different words
(therefore controlled vocabularies must be used)
Anatomical structures may not be named (or the biologist doesn’t know it)
People have selective vision
emage edinburgh mouse atlas of gene expression
To make things worse...
Embryos are 3D
emage edinburgh mouse atlas of gene expression
To make things worse...
Embryos are 3D
Many modifiers are required to describe the subtleties of an
expression pattern
(eg. proximal, distal, lateral, measurements etc)
emage edinburgh mouse atlas of gene expression
To make things worse...
Embryos are 3D
Many modifiers are required to describe the subtleties of an
expression pattern
(eg. proximal, distal, lateral, measurements etc)
Embryos change their morphology
over time (and size)
emage edinburgh mouse atlas of gene expression
To make things worse...
Embryos are 3D
Many modifiers are required to describe the subtleties of an
expression pattern
(eg. proximal, distal, lateral, measurements etc)
Embryos change their morphology
over time (and size)
Zebrafish development
0-24hrs
Donald Kane & Rolf Karlstrom
Max-Planck Institut für Entwicklungsbiologie
Tübingen
1mm
emage edinburgh mouse atlas of gene expression
To make things worse...
Embryos are 3D
Many modifiers are required to describe the subtleties of an
expression pattern
(eg. proximal, distal, lateral, measurements etc)
Embryos change their morphology
over time (and size)
Comprehensively describing the expression pattern of a
gene throughout embryo development using words is
extremely difficult (or impossible?!)
emage edinburgh mouse atlas of gene expression
EMAGE
Use words (where possible) to describe gene expression
emage edinburgh mouse atlas of gene expression
EMAGE
Use words (where possible) to describe gene expression
via an ontology (a controlled descriptive vocabulary)
emage edinburgh mouse atlas of gene expression
EMAGE
Use words (where possible) to describe gene expression
via an ontology (a controlled descriptive vocabulary)
But more uniquely...
also use spatially standardised images to show gene
expression
“A picture says 1,000 words”
emage edinburgh mouse atlas of gene expression
EMAGE database architecture
BIOLOGIST
Java Swing Application
CORBA
Client machine
(PC, MacOSX, Linux, UNIX)
C++ Application Server
Image files
Text data
Server machines
(SUN Solaris)
ObjectStore Server
The database software has client–server architecture. The application-domain information is stored in an ObjectStore database. The database includes C++ server and Java Swing
client software. The C++ server accesses the database and runs on a Sun Solaris server. The Java client software is delivered by Java Web Start or directly through a web browser
and communicates with the C++ server via Corba. Java Interface can be downloaded from the EMAGE homepage and will run on any platform with Java v1.4.2+ installed. Following
installation, the Java interface can be launched from the EMAGE homepage.
emage edinburgh mouse atlas of gene expression
EMAGE database architecture
BIOLOGIST
Java Swing Application
CORBA
Client machine
(PC, MacOSX, Linux, UNIX)
Server machines
(SUN Solaris)
C++ Application Server
Web DAS
Distributed annotation server
Image files
Text data
ObjectStore Server
The database software has client–server architecture. The application-domain information is stored in an ObjectStore database. The database includes C++ server and Java Swing
client software. The C++ server accesses the database and runs on a Sun Solaris server. The Java client software is delivered by Java Web Start or directly through a web browser
and communicates with the C++ server via Corba. Java Interface can be downloaded from the EMAGE homepage and will run on any platform with Java v1.4.2+ installed. Following
installation, the Java interface can be launched from the EMAGE homepage.
emage edinburgh mouse atlas of gene expression
EMAGE database architecture
BIOLOGIST
PROGRAMMER
Java Swing Application
CORBA
Client machine
(PC, MacOSX, Linux, UNIX)
Webservices
Server machines
(SUN Solaris)
C++ Application Server
Web DAS
Distributed annotation server
Image files
Text data
ObjectStore Server
The database software has client–server architecture. The application-domain information is stored in an ObjectStore database. The database includes C++ server and Java Swing
client software. The C++ server accesses the database and runs on a Sun Solaris server. The Java client software is delivered by Java Web Start or directly through a web browser
and communicates with the C++ server via Corba. Java Interface can be downloaded from the EMAGE homepage and will run on any platform with Java v1.4.2+ installed. Following
installation, the Java interface can be launched from the EMAGE homepage.
emage edinburgh mouse atlas of gene expression
EMAGE database spatial framework - the EMAP Digital Atlas
Based on Theiler (1989) and Kaufman (1992)
emage edinburgh mouse atlas of gene expression
Current EMAP models:
F1 (C57BL/6 x CBA)
emage edinburgh mouse atlas of gene expression
Data integration
In EMAGE
eg. TS17
emage edinburgh mouse atlas of gene expression
Data integration
In EMAGE
eg. TS17
Wholemount
emage edinburgh mouse atlas of gene expression
Data integration
In EMAGE
eg. TS17
Wholemount
emage edinburgh mouse atlas of gene expression
Data integration
In EMAGE
eg. TS17
Wholemount
Section
emage edinburgh mouse atlas of gene expression
Data integration
In EMAGE
eg. TS17
Wholemount
Section
emage edinburgh mouse atlas of gene expression
Data integration
In EMAGE
eg. TS17
Wholemount
Section/OPT
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
emage edinburgh mouse atlas of gene expression
Data can be interrogated spatially
emage edinburgh mouse atlas of gene expression
Data can be interrogated spatially - 2D (wholemount data)
QuickTime™ and a
Animation decompressor
are needed to see this picture.
emage edinburgh mouse atlas of gene expression
Data can be interrogated spatially
emage edinburgh mouse atlas of gene expression
Data can be interrogated spatially - 3D (section data)
emage edinburgh mouse atlas of gene expression
Data mapping in EMAGE
emage edinburgh mouse atlas of gene expression
2D wholemount data
Pax3
Ruth Arkell
emage edinburgh mouse atlas of gene expression
2D wholemount data is mapped to a surface view of
the stage-matched embryo model
Pax3
Ruth Arkell
Appropriate view selected
emage edinburgh mouse atlas of gene expression
2D wholemount data is mapped to a surface view of
the stage-matched embryo model
Pax3
Ruth Arkell
Expression levels transferred to model
emage edinburgh mouse atlas of gene expression
MAPaint Warping Interface
Target
Source
Overlay
Standard EMAP embryo model
in situ hybridisation image
of source and target image
emage edinburgh mouse atlas of gene expression
MAPaint Warping Interface
Deformation
Progress in warping visualised with a triangular
mesh
emage edinburgh mouse atlas of gene expression
MAPaint Thresholding Interface
Mapping
Signal Extraction
Gene expression pattern
mapped onto standard
EMAP embryo model
Gene expression pattern
extracted from source image by
thresholding greyscale values
emage edinburgh mouse atlas of gene expression
Section or OPT data is mapped into the 3D space of
the stage matched model
Section Data
OPT data
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
Bmpr1a
Brigid Hogan
Sox9
James Sharpe
emage edinburgh mouse atlas of gene expression
Single section data
Bmpr1a
Brigid Hogan
Yas Furuta
emage edinburgh mouse atlas of gene expression
Single section data
Bmpr1a
Brigid Hogan
Yas Furuta
Equivalent section chosen
from virtual 3D model
emage edinburgh mouse atlas of gene expression
Single section data
Bmpr1a
Brigid Hogan
Yas Furuta
Data transfer by ‘warping’
and subsequent thresholding
emage edinburgh mouse atlas of gene expression
Single section data
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
Bmpr1a
Brigid Hogan
Yas Furuta
Data is held in 3D space
emage edinburgh mouse atlas of gene expression
Serial section data
Bmp4lacZneo
Brigid Hogan
emage edinburgh mouse atlas of gene expression
Serial section data
emage edinburgh mouse atlas of gene expression
Serial section data
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
emage edinburgh mouse atlas of gene expression
OPT data - 3D warping interface
QuickTime™ and a
MPEG-4 Video decompressor
are needed to see this picture.
Fgf8
Diego Aza-Echevarria
Salvador Martinez
emage edinburgh mouse atlas of gene expression
Spatially
mapped
data is
then entered
into the
EMAGE
interface:
emage edinburgh mouse atlas of gene expression
Spatially
mapped
data is
then entered
into the
EMAGE
interface:
emage edinburgh mouse atlas of gene expression
Other data entered in EMAGE:
emage edinburgh mouse atlas of gene expression
Other data entered in EMAGE:
Gene name/symbol
emage edinburgh mouse atlas of gene expression
The combination of spatial and text based data types enable
searching by both space and text...
What
genes
are detected in
spatial region
at Stage X?
emage edinburgh mouse atlas of gene expression
The combination of spatial and text based data types enable
searching by both space and text...
What
genes
are detected in
spatial region
anatomical
component
at Stage X?
emage edinburgh mouse atlas of gene expression
The combination of spatial and text based data types enable
searching by both space and text...
What
genes
are detected in
spatial region
anatomical
component
anatomical components
express selected genes
at Stage X?
emage edinburgh mouse atlas of gene expression
The combination of spatial and text based data types enable
searching by both space and text...
What
genes
are detected in
spatial region
anatomical
component
anatomical components
regions
express selected genes
at Stage X?
emage edinburgh mouse atlas of gene expression
The combination of spatial and text based data types enable
searching by both space and text...
What
genes
are /are not detected in
spatial region
anatomical
component
have a similar expression pattern
anatomical components
regions
express / do not express
selected genes
at Stage X?
emage edinburgh mouse atlas of gene expression
Synexpression
emage edinburgh mouse atlas of gene expression
Synexpression
Gawantka et al, (1998) Mech Dev 77:95 - 141
Niehrs & Pollet (1999) Nature 402:483 - 487
emage edinburgh mouse atlas of gene expression
Synexpression
Gawantka et al, (1998) Mech Dev 77:95 - 141
Niehrs & Pollet (1999) Nature 402:483 - 487
Synexpression Groups:
“Sets of genes that share a complex ‘spatial’ expression pattern
(in multiple tissues) and that function in the same process”
emage edinburgh mouse atlas of gene expression
Synexpression
Gawantka et al, (1998) Mech Dev 77:95 - 141
Niehrs & Pollet (1999) Nature 402:483 - 487
Synexpression Groups:
“Sets of genes that share a complex ‘spatial’ expression pattern
(in multiple tissues) and that function in the same process”
Bmp4 synexpression group:
emage edinburgh mouse atlas of gene expression
Synexpression
Gawantka et al, (1998) Mech Dev 77:95 - 141
Niehrs & Pollet (1999) Nature 402:483 - 487
Synexpression Groups:
“Sets of genes that share a complex ‘spatial’ expression pattern
(in multiple tissues) and that function in the same process”
Bmp4 synexpression group:
Onichtchouk et al, Nature (1999) 410:480-5
emage edinburgh mouse atlas of gene expression
Synexpression
Fgf8 synexpression group:
emage edinburgh mouse atlas of gene expression
Synexpression
zFgf8
zSpry
zSef
mFgf8
mSpry
mSef
Fgf8 synexpression group:
Fürthauer et al (2002) Nat Cell Biol 4: 170-174
xFgf8
xFGFRL1
xFgf8
Hayashi et al (2004) Dev Dyn 230: 700-707
xIsthmin
Pera et al (2002) Mech Dev 116: 169-172
Lin et al (2002) Mech Dev 113: 163-168
emage edinburgh mouse atlas of gene expression
Synexpression
Fgf8 synexpression group:
Sef
Fgf8
Spry (1-4)
Isthmin?
Fgfrl1
emage edinburgh mouse atlas of gene expression
Searching for simple spatial overlaps:
emage edinburgh mouse atlas of gene expression
Searching for simple spatial overlaps:
Database entries
emage edinburgh mouse atlas of gene expression
Searching for simple spatial overlaps:
Query
Database entries
emage edinburgh mouse atlas of gene expression
Searching for simple spatial overlaps:
3 73 7
Query
3 3 3 3
Search results for overlap
emage edinburgh mouse atlas of gene expression
Test Data Set:
emage edinburgh mouse atlas of gene expression
Query Pattern
emage edinburgh mouse atlas of gene expression
Patterns in the set which overlap with
:
emage edinburgh mouse atlas of gene expression
Searching EMAGE for similar spatial patterns:
emage edinburgh mouse atlas of gene expression
Searching EMAGE for similar spatial patterns:
A
B
C
D
E
F
G
H
Database entries
emage edinburgh mouse atlas of gene expression
Searching EMAGE for similar spatial patterns:
A
B
C
D
E
F
G
H
Query
Database entries
emage edinburgh mouse atlas of gene expression
Searching EMAGE for similar spatial patterns:
A
G
H
C
F
D
B
most similar
E
Query
least similar
no overlap
Results (ranked by decreasing similarity)
emage edinburgh mouse atlas of gene expression
Test Data Set:
emage edinburgh mouse atlas of gene expression
Query Pattern
emage edinburgh mouse atlas of gene expression
Patterns in the set which are similar with
Results (in decreasing spatial similarity)
:
emage edinburgh mouse atlas of gene expression
Patterns in the set which are similar with
Query
Emx2
1
Wnt8b
(1.0)
2
Foxg1
5
:
( 0. 337)
Pax1
(0.239)
6
( 0.218)
Wnt7b
3
( 0.287)
Pax6
4
Bmp7
7
( 0.152)
( 0.248)
Otx2
8
Results (in decreasing spatial similarity)
( 0.120)
emage edinburgh mouse atlas of gene expression
Patterns in the set which are similar with
:
Query
1
5
(1.0)
2
( 0. 337)
(0.239)
6
( 0.218)
3
( 0.287)
7
( 0.152)
4
8
( 0.248)
( 0.120)
emage edinburgh mouse atlas of gene expression
Patterns in the set which are similar with
:
(area intersection / area of union - strong regions only)
Query
1
query
Region
(d1)
(1.0)
2
( 0. 337)
(0.239)
6
( 0.218)
3
( 0.287)
4
( 0.248)
target
Region
(d2)
5
7
( 0.152)
8
( 0.120)
emage edinburgh mouse atlas of gene expression
Mouse Brain Organization Revealed through Direct Genome
Scale Transcription Factor Expression Analysis
Paul A. Gray1, 3,9*, Hui Fu2,3*, Ping Luo1,3*, Qing Zhao4, Jing Yu5, Annette Ferrari3,
Toyoaki Tenzen5, Dong-in Yuk4, Eric F. Tsung6,10, Zhaohui Cai6, John A. Alberta3,
Le-ping Cheng1, 3, Yang Liu1, 3, Jan M. Stenman5, M. Todd Valerius5, Nathan
Billings4, Haesun A. Kim2,3,11, Michael E. Greenberg8, Andrew P. McMahon5, David H. Rowitch4,7,
Charles D. Stiles2, 3, and Qiufu Ma1,3
1Department
of Neurobiology and 2 Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
of Cancer Biology and 4Department of Pediatric Oncology, Dana-Farber cancer Institute, 1 Jimmy Fund way, Boston, MA 02115, USA
5Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
6Informatics program, 7Division of Newborn Medicine, and 8Division of Neuroscience, Children’s Hospital, Boston, MA 02115, USA
9Present address, Molecular Neurobiology Laboratory, The Salk Institute, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
10Present address: Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
11Present address, Department of Biological Sciences, Rutgers University, 101 Warren Street, Newark NJ 07102
3Department
*These authors contribute equally to this work.
Science, 306:2255-7
emage edinburgh mouse atlas of gene expression
Wholemounts
Jing Yu, Andy McMahon
emage edinburgh mouse atlas of gene expression
Wholemounts
Jing Yu, Andy McMahon
emage edinburgh mouse atlas of gene expression
‘McMahon’ Data
…map 1800 patterns…
… perform spatial comparisons
between each pattern…
… then do hierarchical clustering
emage edinburgh mouse atlas of gene expression
‘McMahon’ Data
emage edinburgh mouse atlas of gene expression
‘McMahon’ Data
emage edinburgh mouse atlas of gene expression
‘McMahon’ Data
HoxC5
‘McMahon’ Data
HoxC5
HoxD3
HoxB7
HoxB7
HoxC8
HoxC8
emage edinburgh mouse atlas of gene expression
‘McMahon’ Data
Oracle1/Ldb3/Cypher
Meox1
myogenin
(myogenic regulatory factors)
eg. myogenin
maintenance of Z-band
cypher
emage edinburgh mouse atlas of gene expression
Similarity searching in section data
emage edinburgh mouse atlas of gene expression
Alx3
Alx4
Bmp4
Bmpr1a
Bmpr1b
Crabp1
Egr2
Emx1
Emx2
En2
Eya2
Fgf4
Fgf8
Foxc2
Hand1
Hoxa1
Hoxa2
Hoxa3
Hoxb1
Lhx2
Lhx3
Mef2c
Msx1
Msx2
Myl2
Ncam1
Nkx2-5
Nmyc1
Nppa
Nppb
Pax6
Sema3a
Shh
Six3
Slc2a3
Snai1
Sox2
Sox3
Tcfap2
Titf1
Vax1
Wnt1
Wnt7a
emage edinburgh mouse atlas of gene expression
Alx3
Alx4
Bmp4
Bmpr1a
Bmpr1b
Crabp1
Egr2
Emx1
Emx2
En2
Eya2
Fgf4
Fgf8
Foxc2
Hand1
Hoxa1
Hoxa2
Hoxa3
Hoxb1
Lhx2
Lhx3
Mef2c
Msx1
Msx2
Myl2
Ncam1
Nkx2-5
Nmyc1
Nppa
Nppb
Pax6
Sema3a
Shh
Six3
Slc2a3
Snai1
Sox2
Sox3
Tcfap2
Titf1
Vax1
Wnt1
Wnt7a
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
emage edinburgh mouse atlas of gene expression
3D - Searching for simple spatial overlaps:
(Pairwise comparison of significant spatial overlaps based on voxel numbers)
emage edinburgh mouse atlas of gene expression
3D - Searching for similar spatial patterns:
emage edinburgh mouse atlas of gene expression
3D - Searching for similar spatial patterns:
(Pairwise correlations converted to global Euclidian distances: a GLOBAL comparison of all the data in the set)
emage edinburgh mouse atlas of gene expression
Clustering using spatial mapping
A
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
pairwise
global
B
emage edinburgh mouse atlas of gene expression
Clustering using spatial mapping
A
B
X
Y
Z
a
b
g
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
pairwise
global
emage edinburgh mouse atlas of gene expression
Clustering using spatial mapping
A
B
X
Y
Z
a
b
g
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
pairwise
global
emage edinburgh mouse atlas of gene expression
Clustering using spatial mapping
A
B
X
Y
Z
a
b
g
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
pairwise
global
emage edinburgh mouse atlas of gene expression
3D - Searching for similar spatial patterns:
Global pattern comparison
emage edinburgh mouse atlas of gene expression
3D - Searching for similar spatial patterns:
Global pattern comparison
Crabp1
crabp1
egr2
hoxa3
hoxa2
Egr2
Hoxa3
Hoxa2
Hindbrain Cluster
emage edinburgh mouse atlas of gene expression
3D - Searching for similar spatial patterns:
Global pattern comparison
Vax1
Bmpr1b
Bmpr1a
Titf1
Bmp4
Bmp4
Foxc2
Pax6
Pax6
Eye Cluster
Eya2
Sox2
Six3
alx4
bmpr1a
bmpr1b
sox2
eya2
pax6
six3
shh
titf1
vax1
emage edinburgh mouse atlas of gene expression
3D - Searching for similar spatial patterns:
Global pattern comparison
Myl2
Nkx2-5
Mef2C
Nppa
Mef2C
mef2c
myl2
nmyc1
nkx2-5
nppa
nppb
Nppb
Heart Cluster
emage edinburgh mouse atlas of gene expression
‘Curran’ Data
1 embryo, 2 sections each for 42 genes
emage edinburgh mouse atlas of gene expression
‘Curran’ Data
1 embryo, 2 sections each for 42 genes
4800 sections (2400 genes) - currently unannotated
emage edinburgh mouse atlas of gene expression
MRC Human Genetics Unit, Edinburgh
Division of Biomedical Sciences, University of Edinburgh
EMAGE:
Yiya Yang
Nick Burton
Shanmugasundaram Venkataraman
Lorna Richardson
Peter Stevenson
Jeff Christiansen
EMAP:
Margaret Stark
Bill Hill
Jianguo Rao
Albert Burger
Julie Moss
Liz Graham
Allyson Ross
Keo Chanavinout
Guangjie Feng
Nestor Milyaev
Derek Houghton
Ying Cheng
Dave Clements
Chris Tindal
Mehran Sharghi
Xinguin Pi
Jonathan Bard
Matt Kaufman
Mouse Genome Informatics, Jackson Laboratory
Martin Ringwald and the GXD team
Richard Baldock
Duncan Davidson
HGU Bioinformatics:
Phillippe Gautier
Colin Semple
genex.hgu.mrc.ac.uk