Download StemBase

StemBase
Stem Cell Network
Microarray Course, Unit 6
June 2007
Sections
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Introduction to StemBase
Using StemBase
Introduction to Biomarker server
Using the Biomarker server
Introduction to
StemBase
http://www.stembase.ca
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
OHRI – GENOMICS PLATFORM
DNA microarray / SAGE / Proteomics
data
Bioinformatics Group
data
StemBase
PUBLIC
SCN Sample Contributors
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Jane Aubin
Mick Bhatia
John Dick
Connie Eaves
Jacques Galipeau
Alain Garnier
Marina Gertsentein
John Hassell
Keith Humphries
Norman Iscove
Michael McBurney
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Lynn Megeney
James Piret
Derrick Rancourt
Janet Rossant
Michael Rudnicki
Luc Sabourin
JP Tremblay
T. Michael Underhill
Valerie Wallace
Peter Zandstra
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.
Species
Tissue Types
Mouse
184
Retina, 3
Human
44
Muscle, 42
Adipose tissue, 1
Blastocyst, 20
Blood, 5
3 Rat
Bone marrow, 31
Mammary, 14
Kidney, 1
Fibroblast, 4
Brain, 7
Calvaria, 3
Cervical epith., 3
Ciliary margin eye, 4
Fetal cells, 38
Cordblood, 11
Dermis, 1
Embryonic, 42
Genes expressed in:
GO
80%100%
of all
samples
0%20%
of all
samples
Pvalue
GO as name
GO:0030529
1.83E-66 ribonucleoprotein complex
GO:0003723
1.40E-42 RNA binding
GO:0005739
9.43E-31 mitochondrion
GO:0006412
3.03E-28 protein biosynthesis
GO:0044237
4.31E-27 cellular metabolism
GO:0008380
1.79E-22 RNA splicing
GO:0045184
3.50E-22 establishment of protein localization
GO:0016526
3.40E-11 G-protein coupled receptor activity, unknown ligand
GO:0005246
0.00362 calcium channel regulator activity
GO:0007416
0.0134 synaptogenesis
GO:0016358
0.0204 dendrite morphogenesis
GO:0007076
0.0348 mitotic chromosome condensation
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
Human / HGU133
Cord blood
Bone marrow
Dim2
M-O7e Smad7
Cord blood
M-O7e
Peripheral
M-O7e
Fetal
Peripheral
Hela
I6
Cord blood
Hela
Bone marrow
Kidney
Retinal
primary
Myoblasts
Retinal first passage
Myoblasts
differentiated
Dim1
I6
Public web server
http://www.scgp.ca:8080/StemBase/
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.
Method Overview
• Identification
– Find probe sets which appear to divide samples
into two groups  binary classifications
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
• Receiver Operator Characteristic (ROC) curves are
used to generate clusters of probe sets with
expression patterns which can reproduce each
binary classification.
1402235_at
“Pattern X”
1101100101101110
Proposed markers for “Pattern X”
Probe set Score
1402235_at 1.00000
1409748_at 1.00000
1430293_x_at
0.99302
…
1427392_a_at
0.90021
embryonic
osteoblast fibroblast
P19
spheres
hematopoietic
Five fold enrichment on 71 stem cell markers.
From 71 in about 30,000 genes to 49 in 4,449 genes
http://www.ogic.ca/projects/markerserver/enter.php
Pointers
• StemBase. http://www.stembase.ca
• Biomarker server.
http://www.ogic.ca/projects/markerserver
• Thanks for your attention!