Functional Genomics
This is a field of molecular biology that attempts to
describe gene (and protein) functions and interactions.
The “OMICS” Loop
Why Functional Genomics is Important
% of genes with
Completion date
Organism # genes inferred
of genome
function
E. coli 4288 60 1997
yeast 6,600 40 1996
C. elegans 19,000 40 1998
Drosophila 12-14K 25 1999
Arabadopsis 25,000 40 2000
mouse ~30,000? 10-20 2002
human ~30,000? 10-20 2000
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Functional genomics and bioinformatics
• Because of the large quantity of data set produced
by this field and the desire to find biologically
meaningful patterns, Bioinformatics is crucial for
analysis of functional genomics data.
Techniques to Determine the Gene Function
Followings are major approaches used in Functional Genomics:
1. DNA based approach
2. RNA based approach
3. Protein based approach
4. Loss of function technique
5. Computer based approach
1- DNA Based Approach
• Genetic interaction mapping
Systematic pair wise deletion of genes or inhibition
of gene expression can be used to identify genes with
related function.
2- RNA Based Approach
• Gene Chips
A DNA microarray (also commonly known as DNA chip or
biochip) is a collection of microscopic DNA spots attached to
a solid surface.
• Tiling arrays
Genome tiling arrays consist of overlapping
probes designed to densely represent a
genomic region of interest, sometimes as
large as an entire human chromosome. The
purpose is to empirically detect expression
of transcripts or alternatively spliced forms
which may not have been previously
known or predicted.
3- Protein Based Approach
• Yeast Two-hybrid System
A yeast two-hybrid (Y2H) screen tests a "bait" protein against
many potential interacting proteins ("prey") to identify physical
protein–protein interactions.
• Phage display
It uses bacteriophages (viruses
that infect bacteria) to connect
proteins with the genetic
information that encodes them.
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4- Loss of Function Technique
• Gene Knockout Method/ Mutagenesis
A gene knockout (KO) is a genetic technique in which one of an
organism's genes are made inoperative ("knocked out" of the
organism).
• RNAi
RNA interference methods
can be used to transiently
silence or knock down
gene expression.
5- Computer Based Approach
• Rosetta Stone Method
It is based on the hypothesis that some proteins involved in a
given physiological process may exist as two separate genes in
one organism and as a single gene in another.
• Gene Neighborhood Method
Two genes if consistently
found side by side in the
genome of several different
organisms, they are likely to be
functionally linked.
• Sequence Homology
Sequence similarity between two genes is determined by
alignment methods.
Structural Genomics Approach
• Structural genomics seeks to describe the 3-dimensional
structure of every protein encoded by a given genome.
Protein structures are linked with functionality of protein.
