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System Biology. Gustavo de Souza IMM, OUS. October 2013. Scrutinizing global changes. Reductionism VS Holism. The study of biology through systematic perturbation, global read-out of the multifaceted and integration of these data to formulate predictive models.

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system biology

System Biology

Gustavo de SouzaIMM, OUS

October 2013

slide3

Reductionism VS Holism

The study of biology through systematic perturbation, global read-out of the multifaceted and integration of thesedata to formulate predictive models

Ideker et al., Annu. Rev. Genomics Hum. Genet. 2:343-72, 2001.

slide5

Integrating expression data

Ge H et al., 2003.

slide6

Comparing data

Ge H et al., 2003.

slide7

Strategy

Ge H et al., 2003.

slide8

System Biology in Immunology

Amit I et al., 2011

slide9

System Biology in Immunology

Amit I et al., 2011

slide10

System Biology in Immunology

Amit I et al., 2011

slide11

Obvious Challenges

  • Signal VS Noise
  • Biologically relevant VS random effect
  • Integration of discovery- and hypothesis-driven science
  • Integration of technology – biology - computation
slide14

Proteomics capacity as a System Biology tool

Proteomics can reach 86%of Ids predicted by transcriptomics

At the cost of 12 days of analysis

slide19

Take home message

  • System biology is a post-genomic field that focus in global changes within a system.
  • Depends heavily on computational approaches (measurement, statistical validation, integration of thousands of components)
  • Proteomics is still “under development” compared to Genomics/transcriptomics, but has almost comparable throughput in recent years
advanced proteomics

Advanced Proteomics

Gustavo de SouzaIMM, OUS

October 2013

slide22

Relevance of the Proteome

If a gene is transcripted andits mRNA levels goes up, doesthat necessarily means theprotein level that the mRNAtranslates also goes up?

slide30

Super-SILAC

Geiger T et al., 2010

slide31

Spike-In SILAC

Geiger T et al., 2013

slide38

Take home message

- As a descriptive data, proteomics is almost as throughput as transcriptomics (the catch 22 is: it does require very high level of expertise to perform proteomics at higher standards).

- Proteomics is arguably more appropriate than transcriptomicsto elucidate functional studies.

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