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GENE FUCTIONAL MAPPING 
Luciano Milanesi 
Consiglio Nazionale delle Ricerche - ITBA 
E-mail: milanesi@itba.mi.cnr.it 
Raffaella Rizzi 
Politecnico of Milan 
E-mail: rizzi@itba.mi.cnr.it 
KEYWORDS: gene expression, hybridization, oligonucleotide, cDNA, microarray. 
ABSTRACT 
Recently a new methodology based on gene expression studies has been developed to understand the role 
of genes in regulating the biological activity in living organisms. The expression profiles in a living cell 
(e.g. which genes are active and which genes are suppressed) are derived by investigating the images 
produced by fluorescent reactions on nylon membranes or from microscope glass slides. The digitization 
of expression images, by means of digital cameras or flatbed and drum scanners, generates the signal to be 
analyzed. This method is highly parallel and at the same time allows to monitor a high-density panel of 
genes by analyzing single-color and dual-color images (respectively for one cellular population and for 
two different cellular populations). A brief description of the gene expression studies used for microarray 
gene functional mapping and some procedure for the digital image analysis will be presented. 
1. INTRODUCTION 
The first part of the Genome Project will 
probably conclude in year 2003 (Schena et al., 
1996) with the sequencing of the complete 
genome of all living organisms; at present this 
purpose has been settled for a unique eukariotyc 
organism: the yeast Saccharomyces cerevisiae 
(Wodicka et al., 1997). 
The second part of the project will concern the 
investigation of the genome-wide expression of 
living cells (particularly for the 80,000-100,000 
genes of the human cells) to understand the 
protein role in the cellular function thoroughly. 
The traditional gene mapping consists in 
determining the chromosome, which contains 
the particular gene, and the reciprocal positions 
between genes. Types of maps are cytogenetic 
maps (gene is mapped in region which is some 
megabases wide), physical maps (localization of 
identifiable limits) and linkage maps 
(polymorphism of a population). 
The new techniques for gene expression profile 
studies initiate a new kind of mapping: the gene 
functional mapping. 
The gene expression pattern of a single living 
cell in peculiar conditions, is useful to 
acknowledge, on one hand, the health state of 
the cell and, on the other hand, its function. 
That’s why it is very important to study gene 
expression on a suitably wide scale, to monitor 
at the same time, a great number of genes (in the 
future for the entire human genome as biologists 
hope) of several tissue cells, in different 
development phases, in different physiological 
and environmental conditions, treated with 
various chemical substances (to experiment new 
pharmacological targets) and in different states 
of health (cancer cellular lines to determine 
oncogenes and tumor suppresser genes) (Chen et 
al., 1998; Schena et al., 1995, 1996; DeRisi et al., 
1996, 1997; Nguyen et al., 1995; Bernard et al., 
1996; Lockhart etal., 1996; et al., 1997; Wodicka 
etal., 1997). 
The following methods will be based on the 
hybridization reaction of cellular messenger RNA 
with high-density arrays of cDNA clones (Chen 
et al., 1998; Bernard et al., 1996; DeRisi et al., 
1997), even with unknown sequences (Schena et 
al., 1995, 1996), or synthetic oligonucleotide