Update on StemBase, the database of the Stem Cell Genomics Project

Miguel Andrade, OHRI, Ottawa

StemBase

DVD release Oct 2005

Stem Cell Genomics Project

StemBase

DVD release Oct 2005

Stem Cell Genomics Project

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

OGIC – GENOMICS PLATFORMPearl Campbell

Bioinformatics Group

StemBase

samples

data

data

PUBLIC

Yauk CL, Berndt ML, Williams A, Douglas GR. 2004. Comprehensive comparison of six microarray technologies. Nucleic Acids Research. 32(15): p. e124

WorkingStemBase

WorkingStemBase

PublishedStemBase

PublishedStemBase

PublicStemBase

PublicStemBase

Data production

Data production

Bioinformaticsanalysis

Bioinformaticsanalysis

SubmitterSubmitter

Networkinvestigators

Networkinvestigators

4 Approverelease?

4 Approverelease?

1 Sample

2 Data

3 Data

5 Embargo or remove

5 Publish data

YES

NO

4 Monthseach sample

12 months entire StemBase

6 Publicize data

Data sharing model

SCN Sample Contributors• 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

• 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

Blastocyst

Blood

Bone marrow

Brain

Calvaria

Cervix epithelium

Fetal liver

Mammary gland

Muscle

Myoblasts

Neural

Retina

FibroblastsKidney

LarynxLimb bud

Ciliary margin of eye

Adipose Tissue

DermisCord Blood

Embryonic

Embryonic Carcinoma

Data collection191 samples

1/4 Human3/4 Mouse… Rat

StemBase

DVD release 1 Oct 2005

Stem Cell Genomics Project

StemBaseDatabase of gene expression data in mouse and human stem cells

Affymetrix DNA microarray data.185 samples.

Serial Analysis of Gene Expression.6 samples.

Study genes important for stem cell function

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 serverhttp://www.scgp.ca:8080/StemBase/

Data submission to GEO

Required by some journals

Largest gene expression data repository

StemBase: High quality dataFocused on stem cellsMore functionality

GEO as a traffic catch

Data submission to GEO

Dermis

AdiposeNeural

Myoblasts

Bone marrow

Bone marrowMuscle

Myospheres

Bone marrow

Osteoblasts

Retinal primary

Retinal first passageMammospheres

Mammospheres undifferenciated

Neurospheres

Bone marrow

CancerR1 serum64

Cancer

Cancer Embyoid bodies

R1 serum6999 D4D

D4EEmbyoid bodiesJ1C2E

D4AR1V6.5

C2D Embyoid bodiesC2A

Dim1

Dim2

Mouse / MOE430

Carolina Perez-IratxetaCarolina Perez-Iratxeta

Cord blood

Bone marrow

Cord blood

Bone marrowCord blood

Peripheral

PeripheralFetal

Myoblasts

I6

Retinal first passage

Myoblasts differentiated

Retinal primary

HelaHela

M-O7eM-O7e

M-O7e Smad7

Kidney

I6

Human / HGU133

Carolina Perez-IratxetaCarolina Perez-IratxetaDim1

Dim2

Analysis of genes correlated with Oct4

self-renewaltotipotency

Oct4

lineage commitment

ES EB

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 CampbellPearl Campbell

Haem

atop

ioet

ic

Embr

yoni

c

Ost

eobl

asts

Neuro

sphe

res

Cance

r

C2C12

Paul KrzyzanowskiPaul 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.

12h<0h

6h<0h

6h>0h

12h>0h

P1 Egr1P2 Klf4P3 Klf4P4 D930005D10Rik

P5 Pim3P6 Rtn4P7 -P8 Socs3P9 Fblim1P10 Epha5P11 Sfrs5P12 TaglnP13 1190003J15Rik

P14 Herc1P15 Spry4P16 Fblim1P17 MrasP18 Anxa3P19 Zfp54P20 Rbm5P21 4930431H11Rik

P22 KhsrpP23 1110061A14Rik

P24 Rbm14

m. Klf4

s. Khsrp

n. Egr1 o. Sfrs5

c. Socs3

q. Rbm5

r. Zfp54

f. Taglnd. Epha5 (Eph receptor A5)

g. Herc1

a. Fblim1 b. 1190003J15Rik

SPRY HECTcRCC1 WD40 RCC1

TR_THYSOCS box

RRM_1

G-patch

l. D930005D10Rik

e. Pim3

h. Spry4 i. Mras

h. Anxa3

p. Rbm14

RRM_1 RRM_1

j. Rtn4

from down-regulated genes / signaling related

SAM 2Calponin repeat

Annexin repeats

from down-regulated genes

/ nucleotide bindingZn finger domains

Zn finger domains

zf-RanBP

Zn finger domains

from up-regulated genes

Egr1 Socs3

Sfrs5

Zfp54

Klf4

Khsrp

Rbm5

Zinc ion binding (GO:0043167)

Nucleic acid binding

(GO:0003676)

Tagln

Epha5

Fblim1

DNA binding

RNA binding

Herc1

Signal transduction (GO:0007165)

D930005D10Rik

Rtn4

Pim3

1190003J15Rik

Spry4 MrasAnxa3

Rbm14

Protein amino acid phosphorylation (GO:0006468)

Morphogenesis (GO:000653)

Protein modification

(GO:0006464)

Integration of proteomics data

New analysis features

External datasets:More stem cell dataCancer sets (e.g. NCI)Normal tissue

Future

StemBase

DVD release Oct 2005

Stem Cell Genomics Project

Raw microarray data in StemBase as of 23 Oct 2005

154 samples426 replicates

4 DVDs

Lily Jin / Gareth Palidwor

DVD release Oct 2005

ProteomicsLawrence PuenteLynn Megeney

Genomics Core FacilityPearl Campbell

Ottawa Genome CentreMichael Rudnicki (director)William Read (project manager)

Stem Cell Network

Norman Iscove (U of T)Tim Hughes (U of T)

Bioinformatics

Miguel Andrade

Enrique Muro Gareth PalidworCarolina Perez-Iratxeta

Lily Jin (-Sept05)

Christopher Porter Paul KrzyzanowskiKagnew Hailesellasse (-Aug05)

Neal Sanche (03-04)

Andrew Kysyk

Thanks!

http://www.scgp.ca:8080/StemBase

http://www.ottawagenomecenter.ca