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Update on StemBase, the database
of the Stem Cell Genomics Project
Miguel Andrade, OHRI, Ottawa
Stem Cell Genomics Project
StemBase
DVD release Oct 2005
Stem Cell Genomics Project
StemBase
DVD release Oct 2005
The Stem Cell Genomics Project
• Objective: acquire a complete understanding
of the genetic factors that:
– specify stem cell identity and function; and
– regulate commitment and differentiation
• Rationale:
– Stem cells play an essential role in the human body as
they provide the starting material for every organ and
tissue
– Knowledge of regulatory genes acting in and on stem
cells is necessary to exploit their full therapeutic
potential
STEM CELL NETWORK
+20 GROUPS
samples
OGIC – GENOMICS PLATFORM
Pearl Campbell
data
Bioinformatics Group
data
StemBase
PUBLIC
Yauk CL, Berndt ML, Williams A, Douglas GR. 2004. Comprehensive comparison of six
microarray technologies. Nucleic Acids Research. 32(15): p. e124
Data sharing model
4 Months
each sample
Submitter
1 Sample
Data
production
3 Data
2 Data
NO
12 months
entire StemBase
4 Approve
release?
5 Embargo
or remove
YES
Bioinformatics
analysis
Working
StemBase
5 Publish data
Published
StemBase
Network
investigators
6 Publicize data
Public
StemBase
SCN Sample Contributors
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Jane Aubin
Mickie Bhatia
John Dick
Connie Eaves
Jaques Galipeau
Alain Garnier
Marina Gertsenstein
May Griffith
John Hassell
Norman Iscove
Michael McBurney
Rod McInnes
Kelly McNagny
Lynn Megeney
James Piret
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Derrick Rancourt
Janet Rossant
Lawrence Rosenberg
Michael Rudnicki
Luc Sabourin
Guy Savageau
Ruth Slack
Jacques P. Tremblay
Valerie Wallace
T. Michael Underhill
Sue Varmuza
Samuel Weiss
Juan Carlos Zuniga-Pflucker
Peter Zandstra
Data collection
191 samples
Retina
Neural
Myoblasts
Muscle
1/4 Human
3/4 Mouse
… Rat
Adipose Tissue
Blastocyst
Blood
Mammary gland
Bone marrow
Limb bud
Larynx
Kidney
Fibroblasts
Fetal liver
Embryonic
Carcinoma
Brain
Calvaria
Cervix epithelium
Embryonic
Ciliary margin of eye
Cord Blood
Dermis
Stem Cell Genomics Project
StemBase
DVD release 1 Oct 2005
StemBase
Database of gene expression data in
mouse and human stem cells
Study genes important for stem cell function
Affymetrix DNA microarray data.
185 samples.
Serial Analysis of Gene Expression.
6 samples.
Perez-Iratxeta, C., G. Palidwor, C.J. Porter, N.A. Sanche, M.R. Huska, B.P. Suomela,
E.M. Muro, P. Krzyzanowski, E. Hughes, P.A. Campbell, M.A. Rudnicki and M.A.
Andrade. 2005. Study of stem cell function using microarray experiments. FEBS
Letters. 579, 1795-1801.
Usage
(1 Nov 2005)
258 non SCN accounts
3,000 logins
First commercial license
Public web server
http://www.scgp.ca:8080/StemBase/
Data submission to GEO
Data submission to GEO
Required by some journals
Largest gene expression data repository
StemBase:
High quality data
Focused on stem cells
More functionality
GEO as a traffic catch
Mouse / MOE430
V6.5
R1
D4A
Embyoid bodies
C2D
C2A C2E
J1
Embyoid bodies D4E
Myoblasts
Cancer
Cancer
R1 serum64
R1 serum6999
D4D
Embyoid bodies
Cancer
Dim2
Neurospheres
Retinal first passage
Dermis
Adipose
Retinal
primary
Mammospheres
Osteoblasts
Neural
Bone marrow
Bone marrow
Myospheres
Dim1
Bone marrow
Mammospheres
undifferenciated
Muscle
Bone marrow
Carolina Perez-Iratxeta
Human / HGU133
Cord blood
Bone marrow
M-O7e Smad7
Dim2
Cord blood
M-O7e
Peripheral
M-O7e
Fetal
Peripheral
Hela
I6
Cord blood
Bone marrow
Kidney
Hela
Retinal
primary
Myoblasts
Retinal first passage
Dim1
I6
Myoblasts
differentiated
Carolina Perez-Iratxeta
Analysis of genes correlated with Oct4
ES
EB
self-renewal
totipotency
lineage
commitment
Oct4
Hypothesis:
Analysis of genes correlated with Oct4 in stem cells will
allow the identification of genes that are important for
stem cell identity and lineage commitment
Pearl Campbell
Paul Krzyzanowski
Time Series
Time series analysis: differentiation three types of
mESC (R1, J1, V6.5) into embryoid bodies
11 time points: 0hr, 6hr, 12hr, 18hr, 24hr, 36hr, 48h,
4day, 7day, 9day and 14day
Hailesellasse et al. 2005. Search for genes important in mouse embryonic stem cell
differentiation. Submitted.
6h<0h
12h<0h
12h>0h
6h>0h
P1
Egr1
P2
Klf4
P3
Klf4
P4
D930005D10Rik
P5
Pim3
P6
Rtn4
P7
-
P8
Socs3
P9
Fblim1
P10
Epha5
P11
Sfrs5
P12
Tagln
P13
1190003J15Rik
P14
Herc1
P15
Spry4
P16
Fblim1
P17
Mras
P18
Anxa3
P19
Zfp54
P20
Rbm5
P21
4930431H11Rik
P22
Khsrp
P23
1110061A14Rik
P24
Rbm14
b. 1190003J15Rik
a. Fblim1
from down-regulated genes / signaling related
c. Socs3
TR_THY
SOCS box
d. Epha5 (Eph receptor A5)
f. Tagln
e. Pim3
Calponin
repeat
SAM 2
g. Herc1
RCC1
i. Mras
h. Spry4
WD40
SPRY
h. Anxa3
RCC1
HECTc
j. Rtn4
l. D930005D10Rik
Annexin repeats
Zn finger
domains
m. Klf4
n. Egr1
from down-regulated genes
Zn finger
domains
o. Sfrs5
/ nucleotide binding
RRM_1
RRM_1
from up-regulated genes
q. Rbm5
p. Rbm14
RRM_1
zf-RanBP
s. Khsrp
r. Zfp54
Zn finger domains
G-patch
1190003J15Rik
Signal transduction
(GO:0007165)
Fblim1
Spry4
Anxa3
Morphogenesis
(GO:000653)
Zinc ion binding
(GO:0043167)
DNA binding
D930005D10Rik
Rtn4
Tagln
Protein amino acid
phosphorylation
(GO:0006468)
Socs3
Egr1
Zfp54
Mras
Rbm14
Epha5
Pim3
Herc1
Klf4
Rbm5
Nucleic acid
binding
(GO:0003676)
Sfrs5
Khsrp
RNA binding
Protein
modification
(GO:0006464)
Future
Integration of proteomics data
New analysis features
External datasets:
More stem cell data
Cancer sets (e.g. NCI)
Normal tissue
Stem Cell Genomics Project
StemBase
DVD release Oct 2005
DVD release Oct 2005
Raw microarray data in
StemBase as of 23 Oct 2005
154 samples
426 replicates
4 DVDs
Lily Jin / Gareth Palidwor
Ottawa Genome Centre
Michael Rudnicki (director)
William Read (project manager)
Proteomics
Lawrence Puente
Lynn Megeney
Genomics Core Facility
Pearl Campbell
Stem Cell Network
Norman Iscove (U of T)
Tim Hughes (U of T)
Bioinformatics
Enrique Muro
Gareth Palidwor
Carolina Perez-Iratxeta
Neal Sanche
(03-04)
Lily Jin (-Sept05)
Miguel Andrade Kagnew Hailesellasse (-Aug05)
Christopher Porter
Paul Krzyzanowski
Andrew Kysyk
Thanks!
http://www.scgp.ca:8080/StemBase
http://www.ottawagenomecenter.ca