MICROARRAY SYSTEM

A System for Managing Data Produced by DNA-microarray Experiments

Alberto Calvi, Pietro Lovato, Simone Marchesini, Barbara Oliboni

Department of Computer Science, University of Verona, Verona, Italy

Massimo Delledonne, Alberto Ferrarini

Department of Biotechnology, University of Verona, Verona, Italy

Keywords:

Microarray, Microarray data management.

Abstract:

In this paper, we present the Microarray System which is based on a MIAME-compatible database and allows

the users to store and retrieve data produced by experiments made with the DNA-microarray technology.

This system was designed and implemented for managing data coming from the Functional Genomics Centre

(FGC) of the University of Verona.

1 INTRODUCTION

Biological data produced by using the DNA-

microarray technology are usually stored in the form

of tab-delimited text ﬁles or excel spread-sheets pro-

duced by the microarray platform. Further informa-

tion about the experiment, such as the name of the

organism and various properties of the microarray

chip, and people that participate to the experiment,

are stored in different ways. For example, the title

of the ﬁles is used to represent information related to

organisms and samples used in the experiment.

For storing and managing data produced by

microarray experiments, and for accessing and

analysing information, several systems have been pro-

posed (Fang et al., 2009; Zhu et al., 2008; Gattiker

et al., 2009; Marzolf et al., 2006; Demeter et al.,

2007; Vallon-Christersson et al., 2009). Moreover,

with the goal of making data coming from microar-

ray experiments fully available to the research com-

munity, some public online systems have been pro-

posed. The most widely used are Gene Expression

Omnibus (GEO) (Edgar et al., 2002), maintained by

the NCBI, and ArrayExpress (Parkinson et al., 2005),

maintained by the EBI.

Public systems require data standardization for

easier storage and interoperability. The standard that

has been proposed in the literature and is the most

widely used for representing the information related

to a microarray experiment is MIAME (Minimum In-

formation About a Microarray Experiment) (Brazma

et al., 2001). MIAME describes the minimum infor-

mation that has to be provided to ensure that data and

results can be easily interpreted; moreover, data stan-

dardization allows the comparison and the veriﬁcation

of experimental results.

In this paper, we consider data coming from the

Functional Genomics Centre of the University of

Verona (FGC), which works as an internal facility of

the University and collaborates with other national

and international academic institutions. The Cen-

tre is based on a Combimatrix array synthesizer that

produces microarrays carrying either 12000 or 90000

oligonucleotide probes (Maurer et al., 2006), and cur-

rently has collected more than 650 gene expression

experiments performed with more than 40 different

chip designs.

In this context, an ad hoc database system for

storing, managing and querying the huge amount of

microarray data the FGC produces, is needed. The

database should not only store microarray experiment

results, but also descriptions of samples used in the

experiment itself, and the way they were treated. The

Microarray System was designed by considering the

FGC speciﬁc needs. Moreover, it was developed to

meet the MIAME standard to deal with the problem

of sharing experimental results among researchers.

Thus, the system supports at the same time a speciﬁc

analytical method, adopted by the FGC, and the inter-

operability with other institutions.

293

Calvi A., Lovato P., Marchesini S., Oliboni B., Delledonne M. and Ferrarini A..

MICROARRAY SYSTEM - A System for Managing Data Produced by DNA-microarray Experiments.

DOI: 10.5220/0003137202930296

In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS-2011), pages 293-296

ISBN: 978-989-8425-36-2

 2011 SCITEPRESS (Science and Technology Publications, Lda.)

Microarray System

Internet

MIAME database

Design data

Organism and sample data

Experiment and hybridization data

User data

Gal

Feature

Probe MAGE-TAB MAGE-ML

Web Interface

Java Servlets

Java Bean and classes

Array Express

(EBI)

GEO (NCBI)

in_parser / out_parser MAGE parser

Figure 1: Overview of the Microarray System.

The Microarray System allows the user to re-

trieve data about every single microarray experiment

and the associated biological information. Data col-

lected from multiple arrays can be easily accessed;

this means that genes expression of a set of related mi-

croarrays, belonging to a particular biological exper-

iment, can be evaluated. Moreover, the system pro-

tects the information from unauthorized access, use,

modiﬁcation or destruction through an access con-

trol mechanism which, by means of user management

and permission assignment, grants conﬁdentiality, in-

tegrity and availability of data.

2 THE MICROARRAY SYSTEM

The Microarray System is a web application based on

a MIAME compatible database, and achieves two dif-

ferent goals: it allows scientists of the FGC to col-

lect and manage data produced by microarray experi-

ments, and it ensures interoperability among different

facilities by granting the possibility to express data

in the MIAME format. In particular, the system al-

lows users (i) to store data in the database, and man-

age them by interacting with the database itself, (ii)

to extract data by the original ﬁles related to the use

of the Combimatrix array synthesizer, and reconstruct

them by querying the database, and (iii) to represent

data extracted from the database by using MAGE-

TAB (Rayner et al., 2006) and MAGE-ML (Spellman

et al., 2002) standard formats.

Fig. 1 gives an overview of the system. An authen-

ticated user can access, through a web interface, to

data stored in the MIAME database by uploading and

downloading information related to chip design, or-

ganisms, samples, experiment details and hybridiza-

tion data. The same information can be exported, in

the MAGE-TAB or MAGE-ML formats, and conse-

quently uploaded to public repositories, i.e. ArrayEx-

press and GEO, or shared with other facilities.

2.1 The System Architecture

The Microarray System is a web application that has

been developed following the Model-View-Controller

architectural pattern (Leff and Rayﬁeld, 2001) in or-

der to isolate the application logic from the user inter-

face (input and presentation), and to permit indepen-

dent development, testing and maintenance of each

layer.

The part related to the Model is the domain-

speciﬁc representation of the data upon which the ap-

plication operates and consists of a set of Java classes

that manipulate data interacting with a persistent stor-

age mechanism. In our case, data are stored in a re-

lational database implemented in MySQL (Widenius

and Axmark, 2002). The View part, implemented

with the JavaServer Pages (JSP) technology (Berg-

sten, 2003), provides the user with an interface, via

web browser, to interact in a transparent way with all

the information stored in the database. For example,

a user can perform several tasks like the search of

experiment data, the execution of BLAST (Altschul

et al., 1990), or the execution of information retrieval

techniques. The servlet acts as the Controller and is

in charge of the request processing and the creation of

any beans or objects used by the JSP, as well as decid-

ing, depending on the user’s actions, which JSP page

to forward the request to.

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294

Figure 2: The thermal shock experiment page.

2.2 The System Features

The Microarray System allows the management of

data produced by microarray experiments. The Sys-

tem allows users to store and manage information re-

lated to chip design, organisms, samples, experiment

details and hybridization data (see left side of Fig. 1).

Moreover, the System is able to store information

extracted from speciﬁc uploaded ﬁles. Information

about the chip are usually maintained in a GenePix

Array List (GAL) (Zhai, 2001) ﬁle that describes sev-

eral aspects of a microarray design, such as the type of

the chip, the number of spots, their dimension and po-

sition, and the respective probe sequence. GAL ﬁles

are produced by using the Combimatrix GAL File

Tool. The ﬂuorescence data are instead organized in

the tab-delimited text ﬁles named Feature and Probe

ﬁles produced by the specialized software Combima-

trix Microarray Imager that analyzes the scanned mi-

croarray image.

For storing into the database information extracted

from the uploaded (input) GAL, Feature, and Probe

ﬁles we designed and implemented the in parser.

In order to guarantee the backward-compatibility with

external applications used for processing data, the Mi-

croarray System allows the user to reconstruct the

GAL, Feature, and Probe ﬁles starting from data

stored into the database by using the out

parser (see

the central part of Fig. 1).

A user can interact with the system through a web

interface, therefore we had to consider some informa-

tion security aspects in order to realize mechanisms

to protect the information and the system from unau-

thorized access, use, modiﬁcation or destruction.

User creation is performed by the system adminis-

trator in order to bound the number of users accessing

the system and meanwhile to record who performs

operations on data. A system user can insert new

information in the database, being automatically in

charge of them, so he/she becomes responsible of as-

signing access permission for the information to other

users (i.e., he/she can set reading and modifying priv-

ileges).

The search functionality is based on the experi-

ment. From a search web page a user can set a sin-

gle ﬁeld, or a combination of ﬁelds. The entries that

match searching parameters are ﬁltered and showed

according to the privileges the user has on the experi-

ments.

At chip design level, it is possible to launch

BLASTx within the system, to ﬁnd homologies be-

tween genes used to design the array and known

proteins in a database (UniProt/Swiss-Prot (Consor-

tium, 2008)). The result is a tab-delimited text

ﬁle containing a mapping between sequence ids and

the UniProt/Swiss-Prot accession number, as well as

other information about the execution. This ﬁle is

then parsed in order to extract information and store

them into the database of the Microarray System al-

lowing for a future implementation of search feature

of sequence ids to create direct links to the speciﬁc

UniProt/Swiss-Prot online page. The original tab-

MICROARRAY SYSTEM - A System for Managing Data Produced by DNA-microarray Experiments

295

delimited ﬁle is also stored and can be downloaded

by a user for usage with external software or further

analysis.

In Fig. 2 we show the web page of an experiment.

In the left side of the page a menu allows the user

to access to suitable pages either to insert new infor-

mation (i.e. Insert organism, Insert design, etc.), or to

require the visualization of stored data (i.e., Organism

List, Experiment list, etc.).

3 CONCLUSIONS AND FUTURE

WORK

The Microarray System copes with the problem of

managing the large amount of data collected from ex-

periments made with the DNA-microarray technol-

ogy by the FGC of the University of Verona. The

proposed system is able to manage MIAME com-

patible information, achieving the needs of sharing

data with the scientiﬁc community working on DNA-

microarrays.

As future work, we plan to extend the database

for considering other types of microarray, and in or-

der to avoid the use of external applications, we plan

to upgrade the Microarray System by implementing

modules for data normalization and data analysis.

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