StemBase Stem Cell Network Microarray Course, Unit 6 June 2007.
Transcript of StemBase Stem Cell Network Microarray Course, Unit 6 June 2007.
StemBase
Stem Cell Network
Microarray Course, Unit 6
June 2007
Sections
• 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
OHRI – GENOMICS PLATFORMDNA microarray / SAGE / Proteomics
Bioinformatics Group
StemBase
samples
data
data
PUBLIC
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
StemBaseDatabase of gene expression data in mouse and human stem cells
Affymetrix DNA microarray data (225 samples) and SAGE (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.
Species
Tissue Types
184
44
3
Mouse
Human
Rat
Blastocyst, 20
Blood, 5
Bone marrow, 31
Brain, 7
Calvaria, 3
Cervical epith., 3Ciliary margin eye, 4
Cordblood, 11
Dermis, 1
Embryonic, 42
Fetal cells, 38
Fibroblast, 4Kidney, 1
Mammary, 14
Muscle, 42
Retina, 3Adipose tissue, 1
Genes expressed in:
80%-100%of all samples
0%-20%of all
samples mitotic chromosome condensation0.0348GO:0007076
dendrite morphogenesis 0.0204GO:0016358
synaptogenesis0.0134GO:0007416
calcium channel regulator activity0.00362GO:0005246
G-protein coupled receptor activity, unknown ligand 3.40E-11GO:0016526
establishment of protein localization3.50E-22GO:0045184
RNA splicing1.79E-22GO:0008380
cellular metabolism4.31E-27GO:0044237
protein biosynthesis3.03E-28GO:0006412
mitochondrion9.43E-31GO:0005739
RNA binding1.40E-42GO:0003723
ribonucleoprotein complex1.83E-66GO:0030529
GO as namePvalueGO
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
Dim1
Dim2
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
Public web serverhttp://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 hematopoieticP19 spheresfibroblastosteoblast
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!