Biological Integration of Spatial and Temporal Localization of genes in C. Elegans

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Biological Integration of Spatial and Temporal
Localization of genes in C. Elegans

• Cesar A. Hidalgo R.

CCNR University of Notre Dame CCSB, DFCI,
Harvard University
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A brief review of genetics
Gene
Upstream
Downstream
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The Combination of Genes that are ON and OFF
determines the phenotype
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Systems Biology

• RNAi
• MicroArray
• GFP-Localization
• PPI
• Genetic Interactions
• Regulatory Networks

How does the organism work?
-How are these connected? -When are they
expressed? (Condition) -When are they expressed?
(Time) -Where are they expressed? -How do they
turn on? (Regulatory Networks)
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Who is connected with whom..?

• Protein-Protein Interactions

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How do they turn on?

• Regulatory interactions? (Positive)

Gene1
Gene2
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How do they turn on?

• Regulatory interactions? (Negative)

Gene1
Gene2
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What happens when we remove one..?
Knock outs
Any difference.?
Gene1
Gene3

• RNAi
• MicroArray
• GFP-Localization
• PPI
• Genetic Interactions
• Regulatory Networks

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What happens when we remove two..?
Genetic Interactions..?
Gene3
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Under which conditions are they expressed?

• Microarray

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Where are they expressed?

• GFP

Upstream
Downstream
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Where is the field at?

• Collecting data and developing methods..?

PPI Cite Rual et. Al. Ito. El al. Uetz. et.
Al. Steltz et. Al. RNAi Microarray. S. Kim. et.
Al.
Coverage is still very low compared to what is
expected to be out there.
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Where is it going..?
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The Localizome

• A high throughput way to determine
  spatio-temporal expression patterns in c. elegans.

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COPAS Biosort-Profiler Union Biometrica
The Localizome (The Data)
Profile Individuals
Fluorescence
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The Localizome (The Data)
Sort the Population
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The Localizome (The Data)
Build Chronograms
TIME
LENGTH
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The Localizome (Validation)

• Validation (Tissue Specificity)

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The Localizome (Data Formating)
Image Filtering (Pixelization and Linear
Filtering)
Before Filtering
After Filtering
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The Localizome (Validation)

• Validation (Average Image)

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The Localizome (Validation)
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The Localizome (Analysis)

• Correlation
• -PCC-

PCC0.88
PCC0.03
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The Localizome (Analysis)
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The Localizome (Analysis)
P-Value Pharynx 1.4x10-5 Vulva Muscle 3.1x10-4
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Validating Clusters
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What can we use this for?
Are all the interactions found with other methods
veridical..?
Are these expressed in the same place and time?
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Protein-Protein Interactions are biological only
in certain regions
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Regulatory Networks
TF
Promoter
TF
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The Big Picture
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Summary

• Reliable localization data can be produced in a
  high throughput with the profiler technology.
• This data can be used potentially to identify the
  sub-networks involved in different organs and in
  different developmental stages.
• So far we see that the overlap between
  interacting partners tends to be partial.

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Acknowledgments
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Alternative Metrics
Overlap Between Significant Expression Areas
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Same Story
Nerve Ring Pvalue 3x10-3
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When genes come to stage