1. Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk Stem Cell Biology and Bioinformatic Tools DBRM, Karolinska Institutet 18-24 September 2008 Elisabet Andersson, Alistair Chalk

2. Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk hES colony stained for Nanog and SSEA-1 What is a stem cell and why are bioinformatics important tools in studying stem cells and differentiation?

3. Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk Byrne, J. A. Hum. Mol. Genet. 2008 17:R37- 41R; doi:10.1093/hmg/ddn053 Factors such as Nanog, Oct4, Sox2, Klf4, Lin28 are introduced into eg fibroblast and cells are screened for totipotency The Stem Cell - maker of all other cells

4. Embryonic Stem cell Specific set of markers eg: Mouse: Nanog, Oct4, SSEA1, Tra-1-80 human: Nanog, Oct4, SSEA4, Tra-1-60 Characteristics: totipotent in definitive growth differentiation Loss of stem cell markers eg Nanog and Oct4 Induction of more lineage specific markers eg: Ectoderm progenitors: Sox2 Mesoderm progenitors: Brachyury T Endoderm progenitors: Sox17 Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk Multipotent stem cells : Hematopoietic stem cells Neuronal stem cells Hepatic stem cells Muscle stem cells etc1

5. Chen, L. et al. Hum. Mol. Genet. 2008 17:R23-27R; doi:10.1093/hmg/ddn050 Intracellular changes during differentiation Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk

6. Huge data sets are rapidly generated via variety of experimental designs that most stem cell biologists are set out to delineate…… Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk

7. Yeo, G. W. et al. Hum. Mol. Genet. 2008 17:R67-75R; doi:10.1093/hmg/ddn065 Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk What goes on when a stem cell go from A to B to C etc? Temporal aspects = many data points = huge data sets Stem cell – multipotent progentitor – bipotent progenitor – mature cell

8. Spatial aspects = many data points = huge data sets Anterior – posterior Dorsal – ventral Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk

9. medium Other factors influencing: - addition/removal of factors eg Shh, Fgf8, Fgf2, Egf - addition/removal of different medium supplements eg N2, B27 - manufacturer - culture conditions - passage of cells Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk

10. Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk Yeo, G. W. et al. Hum. Mol. Genet. 2008 17:R67-75R; doi:10.1093/hmg/ddn065 Molecular regulation of stem cells DifferentiationStudies Gene expression profile microRNA profile Promoter regulation Epigenetic changes Post-translational Phosphorylations Exon usage etc Massive data generated at many different levels How can this be integrated?

11. Ensembl ArrayExpress ArrayExpressAtlas DAVID PathwayCommons CellDesigner Chip-Chip analysis using Ringo Chipster Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk

12. Dry lab rats (ie bioinformatics) Wet lab Rats (ie biologists) Experimental design Micro array Deep sequencing microRNAs Phylogeny Structural relations System biology Chip-on-Chip Chip-IP Domain identification Drug discovery Analysis of existing databases Data handing Promoter/enhancers genome wide Predicitions Stem Cell Biology and Bioinformatic Tools, DBRM, Karolinska Institutet, 18-24 September 2008 Elisabet Andersson, Alistair Chalk