Cluster-Based Mining of Microarray Data in
PHP/ MYSQL Environment
E. Udoh, S. Bhuiyan
Department of Computer Science
Indiana University-Purdue University
2101 E. Coliseum Blvd, Fort Wayne, IN 46805 USA
Abstract - Extracting biological significance from
a large microarray dataset using data mining
clustering technique is an important process in
bioinformatics. In this paper, a microarray dataset
(matrix 504 x 227) made available by SAMSI
institute, was used as the base sample to develop a
new demo web-based clustering system that
exploits the improved efficiency and functionality
of PHP/MYSQL technology. The clustering
algorithms and robustness of PHP/MYSQL
produced categorized microarray data that can be
associated with diseases with improved
visualizations.
Keywords - Data Mining, Microarray, Clustering
Dendrogram, and PHP/MYSQL.
I. INTRODUCTION
Microarray technology generates extremely large
gene expression dataset (hundreds of rows and
columns) in a single biological experiment (Fig.
1). The gene expression patterns provide
unprecedented information on human disease,
aging, drug, mental illness, diet and many other
clinical matters, because they correlate strongly
with function. In the medical world, microarray
has paved the way for a new era of genetic
screening, testing and diagnostics [7]. However,
the dataset often contains missing values, and
exhibits high dimensional attributes, i.e. large
number of genes with relatively small number of
samples [1]. It is cumbersome to manually
examine these large dataset for biological
significance, hence the need for automation (e.g.
using clustering techniques) to reduce the
quantity of data to a manageable level [2, 3].
Clustering techniques can determine intrinsic
grouping in a set of microarray data using
distance or conceptual measures. To determine
membership in a cluster, clustering algorithms
evaluate distance between a point and the cluster
centroid. The output is basically a statistical
description of the cluster centroid with the
number of components in each cluster. However,
197
T. Sobh and K. Elleithy (eds.), Advances in Systems, Computing Sciences and Software Engineering, 197–200.
© 2006 Springer.
domain knowledge is useful to formulate
appropriate measure in a clustering algorithm,
which may be exclusive, overlapping,
hierarchical or probabilistic.
There are several clustering algorithms to
process and establish relationships in large
dataset generated by microarray experiments [4].
These algorithms can be used to determine what
group a particular genetic sample belongs to and
the tendency for certain clusters to be associated
with certain characteristics. This helps to
eliminate less relevant dimensions or genetic
characteristics. In this paper, six algorithms were
applied, e.g. un-weighted pair group centroid,
weighted pair group centroid or ward’s method
to achieve clustering of the samples [5]. These
different algorithms can be applied individually
or compared, and a suitable one chosen for the
investigation.
The microarray data in Fig. 1, made available by
SAMSI institute, was used for this project. The
data consist of a series of genetic profiles for
breast, prostrate, liver, colon, kidney, lung, ovary
and testis cancer (matrix 504 x 227). Some of the
cell samples are malignant while others are
normal. The data are log-transformed, with row
and column means subtracted (with positive
values showing well expressed gene, while
negative values indicate non-expression of gene).
The used data have been subjected to singular
value decomposition by authors in [2] as an
effective way to provide dimensionality
reduction, and eventual elimination of less
relevant data [7, 10].
The main thrust of this project is to cluster
microarray samples with the rich visualization
features in the PHP/MYSQl development
environment [6] as the displays in this project
attest to. PHP, an open source, server-side
scripting language, allows user to easily develop
a robust and dynamically generated page
quickly. PHP is cross-platform and easy to learn
with well balanced memory and server load.
 198 UDOH AND BHUIYAN

The improved visualization features are
attractive to any bioinformatics programmer,
since the representations are intuitive.
II. ANALYSIS and DESIGN
In the first phase to develop bioinformatics
software in PHP/MYSQl environment, this
clustering system was developed in a Linux
server environment hosting Tomcat 5.0, PHP
5.0, MySQL 4.1 and Ghostscript 8.15. The base
technology used for the analysis and design are
the server-side scripting language (PHP) and
MySQL database for persistence storage. On
execution, the PHP code retrieves the microarray
data from the MYSQL database. It converts the
data into a usable format, and then passes the
output to the clustering software, which in turn
sends the result to a dendrogram and ghostscript
programs for visualization. Some of the
clustering algorithms programmed, include
single link, complete link, group average,
weighted average, weighted centroid and ward’s
method (Fig. 2).
As can be gleaned from Fig. 2, the PHP code
calls the mathematical algorithms to perform the
clustering, as well as provide an easy to use
interface to the system. The user will be able to
specify a variety of parameters or algorithms
using the web based interface, while the results
of the clustering can be presented by showing
which clusters are included in particular groups
(Fig. 2). The program shows the percentages of
each cluster with or without the cancer
malignancy. For example, few clusters may be
used and the percentages for cancer within those
groups may be too mixed with normal samples
(such as a 30% cancerous 70% normal) within a
cluster. In such a scenario, the number of clusters
may be increased to allow a better level of
granularity when clustering. Attribute grouping
and associative clustering explain similar
dependencies and also offer improved
classification of such genes [8, 9]. Below is a
dendrogram produced for the analyzed sample
(Fig. 3).
Cancerous samples are indicated by arrows.
These cancerous samples are all in the first
group, with some few normal samples. It is clear
in this example that almost all of the cancer
samples are present in the first group, with a very
high probability that any sample in that group
will be cancerous (Fig. 3). A variation of this
dendrogram can be obtained if another algorithm
is selected (Fig. 4).

34449_at 35150_at
Id Sample_Tissue_Site Sample_General_Pathologic_Category CASP2 TNFRS
72 LIVER, NOS NORMAL -0.64565 -0.71759
77 COLON, NOS NORMAL 0.38159 -0.32849
79 KIDNEY, NOS MALIGNANT 0.83026 -0.2525
83 LIVER, NOS MALIGNANT 0.047638 -0.81221
91 KIDNEY, NOS MALIGNANT -0.22587 -0.45274
96 KIDNEY, NOS NORMAL -0.0528 -0.21131
98 LUNG, NOS MALIGNANT -0.02914 -0.2353
100 COLON, NOS MALIGNANT 0.65866 0.78431
101 LUNG, NOS NORMAL 0.23735 0.003307
109 LIVER, NOS MALIGNANT -0.3751 -0.10789
117 LIVER, NOS NORMAL -1.0638 -0.84062
118 COLON, NOS NORMAL -0.88117 -0.7941
124 LIVER, NOS NORMAL 0.073264 -0.29181

Fig. 1: A cross-section of a microarray dataset used for the design of the system
(http://www.samsi.info/200304/dmml/web-internal/bio/data.html)
 CLUSTER-BASED MINING OF MICROARRAY DATA 199

Fig. 2: Web interface to the cluster program.

Fig. 3: A dendrogram of microarray data (Arrow indicates cancerous sample).

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III. CONCLUSION
The process of finding relevant genetic markers
in a large microarray dataset is a difficult task.
By reducing the amount of data using data
mining technique like clustering, the task is
made a lot easier. This paper exploited the
improved functionality of PHP/MYSQL
programming environment to design a new demo
cluster program. It will be refined in the future to
serve the bioinformatics community better. The
PHP/MYSQL programming is certainly
attractive to the bioinformatics programming
community.
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