A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets.
BACKGROUND
As the number of publically available microarray experiments increases, the ability to analyze extremely large datasets across multiple experiments becomes critical. There is a requirement to develop algorithms which are fast and can cluster extremely large datasets without affecting the cluster quality. Clustering is an unsupervised exploratory technique applied to microarray data to find similar data structures or expression patterns. Because of the high input/output costs involved and large distance matrices calculated, most of the algomerative clustering algorithms fail on large datasets (30,000 + genes/200 + arrays). In this article, we propose a new two-stage algorithm which partitions the high-dimensional space associated with microarray data using hyperplanes. The first stage is based on the Balanced Iterative Reducing and Clustering using Hierarchies algorithm with the second stage being a conventional k-means clustering technique. This algorithm has been implemented in a software tool (HPCluster) designed to cluster gene expression data. We compared the clustering results using the two-stage hyperplane algorithm with the conventional k-means algorithm from other available programs. Because, the first stage traverses the data in a single scan, the performance and speed increases substantially. The data reduction accomplished in the first stage of the algorithm reduces the memory requirements allowing us to cluster 44,460 genes without failure and significantly decreases the time to complete when compared with popular k-means programs. The software was written in C# (.NET 1.1).


BACKGROUND
The program is freely available and can be downloaded from http://www.amdcc.org/bioinformatics/bioinformatics.aspx.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Sharma
Ashok
A
Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta, GA, USA.
Podolsky
Robert
R
Zhao
Jieping
J
McIndoe
Richard A
RA
D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods; D012984:Software