Gene expression can be analyzed using techniques like microarrays and SAGE. A microarray uses DNA probes attached to a solid surface to detect gene sequences via hybridization. SAGE involves isolating mRNA, ligating linkers, and sequencing short tag sequences to profile overall gene expression patterns in a quantitative way. Microarrays and SAGE are useful for applications like gene discovery, disease diagnosis, and analyzing differences in gene expression between cell types.

1. BY
K. THANGA MALLIKA
I M.Sc., MICROBIOLOGY

2.  GENE : A gene is a sequence of DNA or RNA that
codes for a molecule that has a function.
 GENOME : The complete set of genes or genetic
material present in a cell or organism.

3.  It is the process by which information is converted
into the structures and functions of a cell by a process
 During gene expression, the DNA is first copied into
RNA. The RNA can be directly functional or be the
intermediate template for a protein synthesis.

5. Gene expression can be seen through several techniques:
1. cDNA microarray
2. Microarray
3. SAGE

6.  A microarray is a set of short Expressed Sequence Tags
(ESTs) made from a cDNA library of a set of known
gene loci.
 The ESTs are spotted onto a coverslip sized glass plate,
as 8×12 array.
 Microarrays are of many thousand ESTs are possible.

7.  DNA microarray is also known as DNA chip or
biochip.
 DNA microarrays are solid supports, usually of glass
or silicon, upon which DNA is attached in an
organized grid fashion.
 Each spot of DNA is called a probe, represents a single
gene.

9.  The principles behind microarrays is hybridization
between two DNA strands.
 Using this technology, the presence of one genomic or
cDNA sequence in 1,00,000 or more sequences can be
screened in a hybridization.

13. Types of DNA chips:
1. cDNA based microarray
2. Oligonucleotide based microarray

14.  Gene expression
 Disease diagnosis
 Drug discovery
 Toxicological research
 Comparative genomic hybridization
 Gene expression profiling

15.  This type of chips are prepared by using cDNA, it is
called cDNA chips or cDNA microarray or probe DNA.
 The cDNAs are amplified by using PCR.
 Then these are immobilized on to a solid support
made up of nylon filter of glass slide (1×3 inches).

16.  The probe DNA are looked into a spotting spin by
capillary action.
 The small volume of this DNA preparation is spotted
on solid surface making physical contact between
these two.
 DNA is delivered mechanically or by robotic manner.

18. SAGE: Serial Analysis of Gene expression
 SAGE is an approach that allows rapid and detailed
analysis of overall gene expression patters.
 SAGE provides quantitative and comprehensive
expression profiling in a given cell population.
 An overview of a cell’s complete gene activity.

19.  SAGE is mainly based upon two principles:
representation of mRNA by short sequence tags and
concentration of these tags for cloning to allow the
efficient sequencing tags.
 To explain the gene expression profile of the cell, they
would have to conduct several cDNA sequencing
reactions.

20.  Isolation of mRNA of a sample (eg: tumor).
 Linkers are added to each and the RNA is converted to
cDNA by RT-PCR.
 Following this, the linkers, containing restriction sites
are digested with the appropriate restriction enzymes
and the sticky ends are ligated together to form
concatamers.

22. SAGE resources:
 SAGE data
 SAGE tag to gene maps
 SAGE Protocol and software
Useful links:
 SAGE gene
 Download cancer SAGE data
 University of Tokyo

23.  Used in comparative expression studies to identify
differences in gene expression between two or more
cellular sources .
 Gene discovery.
 Analysis of cardiovascular gene expression.
 Profiling of human diseases.
 Provides quantitative data on both known and
unknown genes.