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

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 http://www.systemsbiology.org/Systems_Biology_in_Depth Sunday, November 18, 2018 L519 Bioinformatics Project Lecture: Indigene

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

L519 Bioinformatics Project Lecture: Indigene Trends Genet. 2003 Oct;19(10):551-60.   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

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

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

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

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

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

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

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

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

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

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

L519 Bioinformatics Project Lecture: Indigene Thanks very much! email 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

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. 2003 Oct;19(10):551-60.   Integrating 'omic' information: a bridge between genomics and systems biology. Ge H, Walhout AJ, Vidal M. This is a picture of my dog http://home.arcor.de/chatterji/projekte/gfe/grafiken/c-elegans.jpg http://hdlighthouse.org/see/research/drosophila_200.jpg http://oligos.molgen.mpg.de/yeast.gif Sunday, November 18, 2018 L519 Bioinformatics Project Lecture: Indigene