Biological Integration of Spatial and Temporal Localization of

genes in C. ElegansCesar A. Hidalgo R.

CCNR University of Notre Dame & CCSB, DFCI, Harvard University

mR

NA

A brief review of genetics

GenePromoter

Transcription Factor

Polymerase

Upstream Downstream

Genes are not always on

The Combination of Genes that are ON and OFF determines the phenotype

Systems Biology

-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)

How does the organism work…?

Who is connected with whom..?

Protein-Protein Interactions

How do they turn on?

Regulatory interactions…? (Positive)

Gene1

Gene2

Polymerase

Polymerase

How do they turn on?

Regulatory interactions…? (Negative)

Gene1

Gene2

Polymerase

Polymerase

What happens when we remove one..?

Knock outs

Gene1 Gene2 Gene3

Any difference….?

What happens when we remove two..?

Genetic Interactions..?

Gene1 Gene2 Gene3

Under which conditions are they expressed?

Microarray

Where are they expressed?

GFP

GenePromoter

Transcription Factor

Polymerase

Upstream Downstream

Gene Encoding GFP

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.

Where is it going..?

PPI

Co-Expression

Localization

The Localizome

A high throughput way to determine spatio-temporal

expression patterns in c. elegans.

COPAS Biosort-Profiler Union Biometrica

Flu

ores

cenc

e

The Localizome (The Data)Profile Individuals

Sort the PopulationThe Localizome (The Data)

L1 larvae

Adults

crm-1

TIME

LENGTH

The Localizome (The Data)

Build Chronograms

The Localizome (Validation)

Validation (Tissue Specificity)

The Localizome (Data Formating)

Image Filtering (Pixelization and Linear Filtering)

Before FilteringAfter Filtering

The Localizome (Validation)

• Validation (Average Image)

Average Expression | Annotation

Average Expression | All Annotations

The Localizome (Validation)

The Localizome (Analysis)

Correlation

-PCC-

PCC=0.03PCC=0.88

The Localizome (Analysis)

The Localizome (Analysis)

P-Value

Pharynx : 1.4x10-5

Vulva Muscle: 3.1x10-4

Annotations

P-ValueEmbryo: 1.4x10-2

Validating Clusters

What can we use this for…?

Are these expressed in the same place

and time…?

Are all the interactions found with other methods

veridical..?

Protein-Protein Interactions are biological only in certain regions

Regulatory Networks

Promoter

TF

TF

Pharynx

The Big Picture

EmbryoAdult

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.

Acknowledgments

Alternative Metrics

Overlap Between Significant

Expression Areas

Same Story

Nerve Ring

Pvalue = 3x10-3

When genes come to stage