StemBase

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StemBase

• Stem Cell Network
• Microarray Course, Unit 6
• June 2007

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Sections

• Introduction to StemBase
• Using StemBase
• Introduction to Biomarker server
• Using the Biomarker server

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Introduction to StemBase
http//www.stembase.ca
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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

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STEM CELL NETWORK 20 GROUPS
samples
OHRI GENOMICS PLATFORM DNA microarray / SAGE /
Proteomics
data
Bioinformatics Group
data
StemBase
PUBLIC
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SCN Sample Contributors

• Jane Aubin
• Mick Bhatia
• John Dick
• Connie Eaves
• Jacques Galipeau
• Alain Garnier
• Marina Gertsentein
• John Hassell
• Keith Humphries
• Norman Iscove
• Michael McBurney

• Lynn Megeney
• James Piret
• Derrick Rancourt
• Janet Rossant
• Michael Rudnicki
• Luc Sabourin
• JP Tremblay
• T. Michael Underhill
• Valerie Wallace
• Peter Zandstra

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StemBase
Database of gene expression data in mouse and
human stem cells
Study genes important for stem cell function
Affymetrix DNA microarray data (225 samples) and
SAGE (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.
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Species
Tissue Types
Mouse
184
Retina, 3
Adipose tissue, 1
Human
Blastocyst, 20
44
Blood, 5
Muscle, 42
3
Rat
Bone marrow, 31
Mammary, 14
Brain, 7
Kidney, 1
Fibroblast, 4
Calvaria, 3
Cervical epith., 3
Ciliary margin eye, 4
Fetal cells, 38
Cordblood, 11
Dermis, 1
Embryonic, 42
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Genes expressed in
80-100 of all samples 0-20 of all samples
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Mouse / MOE430
R1
D4A
V6.5
Embyoid bodies
C2D
C2E
C2A
J1
Embyoid bodies
D4E
Cancer
R1 serum6999
D4D
Myoblasts
Embyoid bodies
Cancer
R1 serum64
Cancer
Neurospheres
Retinal primary
Dim2
Mammospheres
Retinal first passage
Mammospheres undifferenciated
Dermis
Osteoblasts
Neural
Adipose
Muscle
Bone marrow
Bone marrow
Bone marrow
Myospheres
Bone marrow
Dim1
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Human / HGU133
Cord blood
Bone marrow
M-O7e Smad7
Cord blood
M-O7e
Dim2
Peripheral
M-O7e
I6
Fetal
Cord blood
Peripheral
Bone marrow
Kidney
Hela
Hela
I6
Retinal primary
Myoblasts
Myoblasts differentiated
Retinal first passage
Dim1
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Public web server
http//www.scgp.ca8080/StemBase/
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Marker detection
Use microarray data to identify probe sets that
can act as markers. What and how they mark is a
separate issue.
Krzyzanowski and Andrade (2007) Identification of
novel stem cell markers using gap analysis of
gene expression data. Submitted.
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Method Overview

• Identification
• Find probe sets which appear to divide samples
  into two groups ? binary classifications

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Method Overview

• Identification
• Find probe sets which appear to divide samples
  into two groups ? binary classifications

• Cluster expansion
• Identify clusters of probe sets which support
  binary classifications

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• Receiver Operator Characteristic (ROC) curves are
  used to generate clusters of probe sets with
  expression patterns which can reproduce each
  binary classification.

Proposed markers for Pattern X Probe
set Score 1402235_at 1.00000 1409748_at 1.00000 1
430293_x_at 0.99302 1427392_a_at 0.90021
1402235_at Pattern X 1101100101101110
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fibroblast
osteoblast
embryonic
hematopoietic
P19
spheres
Five fold enrichment on 71 stem cell markers.
From 71 in about 30,000 genes to 49 in 4,449
genes
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http//www.ogic.ca/projects/markerserver/enter.php
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Pointers

• StemBase. http//www.stembase.ca
• Biomarker server. http//www.ogic.ca/projects/mark
  erserver
• Thanks for your attention!