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
Microarray, Microarray data management.
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.
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.
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
MIAME database
Design data
Organism and sample data
Experiment and hybridization data
User data
Web Interface
Java Servlets
Java Bean and classes
Array Express
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.
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
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.
BIOINFORMATICS 2011 - International Conference on Bioinformatics Models, Methods and Algorithms
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-
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-
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
delimited file is also stored and can be downloaded
by a user for usage with external software or further
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.).
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-
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.
Altschul, S., Gish, W., Miller, W., Myers, W., and Lipman,
D. (1990). Basic Local Alignment Search Tool. J.
Mol. Biol., 215:403–410.
Bergsten, H. (2003). JavaServer Pages, 3rd Edition.
O’Reilly & Associates, Inc., Sebastopol, CA, USA.
Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G.,
and Spellman, P. (2001). Minimum Information about
a Microarray Experiment (MIAME) - toward stan-
dards for microarray data. Nature Genetics, 29:365
– 371.
Consortium, T. U. (2008). The Universal Protein Reasource
(UniProt). Nucleic Acids Res., 36:D190–D195.
Demeter, J., Beauheim, C., Gollub, J., Hernandez-
Boussard, T., Jin, H., Maier, D., Matese, J., Nitzberg,
M., Wymore, F., Zachariah, Z., Brown, P., Sherlock,
G., and Ball, C. (2007). The stanford microarray
database: implementation of new analysis tools and
open source release of software. Nucl Acids Res,
Edgar, R., Domrachev, M., and Lash, A. (2002). Gene
Expression Omnibus (GEO): NCBI gene expressione
and hybridation array data repository. Nucleic Acids
Research, 30:207–210.
Fang, H., Harris, S., Su, Z., Chen, M., Qian, F., Shi, L.,
Perkins, R., and Tong, W. (2009). Arraytrack: An fda
and public genomic tool. Methods Mol Biol, 563:379–
Gattiker, A., Hermida, L., Liechti, R., Xenarios, I., Collin,
O., Rougemont, J., and Primig, M. (2009). Mimas 3.0
is a multiomics information management and annota-
tion system. BMC Bioinformatics, 10:151.
Leff, A. and Rayfield, J. (2001). Web-Application Devel-
opment Using the Model/View/Controller Design Pat-
tern. Enterprise Distributed Object Computing Con-
ference, IEEE International, 0:0118.
Marzolf, B., Deutsch, E., Moss, P., Campbell, D., John-
son, M., and Galitski, T. (2006). Sbeams-microarray:
database software supporting genomic expression
analyses for systems biology. BMC Bioinformatics,
Maurer, K., Cooper, J., Caraballo, M., Crye, J., Suciu, D.,
Ghindilis, A., Leonetti, J., Wang, W., Rossi, F., St
A., Larson, C., Gao, H., Dill, K., and McShea, A.
(2006). Electrochemically generated acid and its con-
tainment to 100 micron reaction areas for the produc-
tion of dna microarrays. PLoS ONE, 1(1):e34.
Parkinson, H., Sarkans, U., Shojatalab, M., Abeygunawar-
dena, N., Contrino, S., Coulson, R., Farne, A., Lara,
G. G., Holloway, E., Kapushesky, M., Lilja, P.,
Mukherjee, G., Oezcimen, A., Rayner, T., Rocca-
serra, P., Sharma, A., Sansone, S., and Brazma, A.
(2005). ArrayExpress a public repository for mi-
croarray gene expression data at the EBI. Nucleic
Acids Research, 33:553–555.
Rayner, T., Rocca-Serra, P., Spellman, P., Causton, H.,
Farne, A., Halloway, E., Irizarry, R., Liu, J., Maier, D.,
Miller, M., Petersen, K., Quackenbush, J., Sherlock,
G., Stoeckert, C., White, J., Whetzel, P., Wymore,
F., Parkinson, H., Sarkans, U., Ball, C., and Brazma,
A. (2006). A simple spreadsheet-based, MIAME-
supportive format for microarray data: MAGE-TAB.
BioMed Central, 7:18.
Spellman, P., Miller, M., Stewart, J., Troup, C., Sarkans,
U., Chervitz, S., Bernhart, D., Sherlock, G., Ball,
C., Lepage, M., Swiatek, M., Marks, W., Goncalves,
J., Markel, S., Iordan, D., Shojatalab, M., Pizarro,
A., White, J., Hubley, R., Deutsch, E., Senger, M.,
Aronow, B., Robinson, A., Bassett, D., Stoeckert, C.,
and Brazma, A. (2002). Design and implementa-
tion of microarray gene expression markup language
(MAGE-ML). Genome Biology, 3(9):research0046.1–
Vallon-Christersson, J., Nordborg, N., Svensson, M., and
Hakkinen, J. (2009). Base - 2nd generation software
for microarray data management and analysis. BMC
Bioinformatics, 10(1):330.
Widenius, M. and Axmark, D. (2002). Mysql Reference
Manual. O’Reilly & Associates, Inc., Sebastopol, CA,
Zhai, J. (2001). Making GenePix Array List (GAL) Files.
Making GAL Files.pdf.
Zhu, Y., Zhu, Y., and Xu, W. (2008). Ezarray: a web-
based highly automated affymetrix expression array
data management and analysis system. BMC Bioin-
formatics, 9:46.
BIOINFORMATICS 2011 - International Conference on Bioinformatics Models, Methods and Algorithms