1. Indigene Project: Systems Biology Project
Memo Dalkilic School of Informatics/Drosophila Genome Resource Center ©MMDalkilic 2005

2. L519 Bioinformatics Project Lecture: Indigene
“Systems biology is the science of discovering, modeling, understanding and ultimately engineering at the molecular level the dynamic relationships between the biological molecules that define living organisms
Leroy Hood
Institute for Systems Biology
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

3. L519 Bioinformatics Project Lecture: Indigene
Outline
Background
Elements of Project
Initial Outcome
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

4. L519 Bioinformatics Project Lecture: Indigene
Trends Genet Oct;19(10):
  Integrating 'omic' information: a bridge between genomics and systems biology. Ge H, Walhout AJ, Vidal M.
What is “systems biology”?
no standard definition yet
rethink reductionist approach
 the majority of gene products work en masse
availability of high-throughput gene product screens
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

5. L519 Bioinformatics Project Lecture: Indigene
What is “systems biology”?
Holistic approach
Assemblage of different (modular) perspectives of systems
people
meteorology
disease
fossil
timeline {
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

6. L519 Bioinformatics Project Lecture: Indigene
Biological processes can be modeled as complex networks of interconnected components. …
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

7. L519 Bioinformatics Project Lecture: Indigene
Modules
transcriptome
proteome
(‘omic’) approaches include
 protein–protein
 protein–DNA (interactome mapping)
 systematic phenotypic analyses (phenome mapping)
 transcript or protein localization mapping (localizome mapping)
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

8. L519 Bioinformatics Project Lecture: Indigene
Data Integration Problem
how is data meaningfully
integrated
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

9. L519 Bioinformatics Project Lecture: Indigene
Human to human 99.9%
Human to Chimp 98%
Human to Mouse 84.9%
Human to Cow 87.1%
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

10. Lots of other organisms to integrate too
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

11. Example of possibility—checking a hypothesis
(a) An interaction network of Snz–Sno proteins of S. cerevisiae. The nodes represent proteins and the lines represent yeast two-hybrid (Y2H) interactions. The red nodes represent proteins that correspond to genes in one transcriptome cluster, whereas the green nodes represent proteins that correspond to genes belonging to a different cluster. The existence of two stable complexes can be hypothesized based on the integrated data.
(b) The genes NTH1 and YLR270W have similar expression profiles (upper panel). Red indicates upregulation and green indicates downregulation. mRNA expressions of both genes are upregulated during heat shock and other forms of stress. Deletions of NTH1 and YLR270W each confer similar heat-shock sensitive phenotypes (lower panel).
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

12. “Another” perspective of systems biology
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

13. How are the data related?
Essential Aspects of a systems biology project
How are the data related?
What kind of model? What kind of inferencing? Is the data validated? Is there sufficient reason to use the network?
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

14. How is static data interpreted since it’s a dynamic system?
Significant Challenges
How is static data interpreted since it’s a dynamic system?
How do we deal with low-resolution quality? How do we treat missing data?
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

15. L519 Bioinformatics Project Lecture: Indigene
Thanks very much!
me if you’d like to discuss anything
Acknowledgements (no special order)
Justen Andrews Haixu Tang Sun Kim Jim Costello
Rupali Patwardhan
Junguk Hur
Sumit Middha
Brian Ead,
Keval Mehta
John Colbourne
Amit Saple
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene

16. L519 Bioinformatics Project Lecture: Indigene
ATTRIBUTION of IMAGES
The following images were taken from other web presentations , but no author could be found:
Several of the figures were taken from:
Trends Genet Oct;19(10):
  Integrating 'omic' information: a bridge between genomics and systems biology. Ge H, Walhout AJ, Vidal M.
This is a picture of my dog
Sunday, November 18, 2018
L519 Bioinformatics Project Lecture: Indigene