KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis

Details KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis

2009-04-13

arxiv.org/abs/0904.1931v1

Computer Science

Databases

International Conference on Bioinformatics and Biomedical Engineering (iCBBE), 2009

Scientific paper

Subspace clustering has gained increasing popularity in the analysis of gene expression data. Among subspace cluster models, the recently introduced order-preserving sub-matrix (OPSM) has demonstrated high promise. An OPSM, essentially a pattern-based subspace cluster, is a subset of rows and columns in a data matrix for which all the rows induce the same linear ordering of columns. Existing OPSM discovery methods do not scale well to increasingly large expression datasets. In particular, twig clusters having few genes and many experiments incur explosive computational costs and are completely pruned off by existing methods. However, it is of particular interest to determine small groups of genes that are tightly coregulated across many conditions. In this paper, we present KiWi, an OPSM subspace clustering algorithm that is scalable to massive datasets, capable of discovering twig clusters and identifying negative as well as positive correlations. We extensively validate KiWi using relevant biological datasets and show that KiWi correctly assigns redundant probes to the same cluster, groups experiments with common clinical annotations, differentiates real promoter sequences from negative control sequences, and shows good association with cis-regulatory motif predictions.

Affiliated with

Also associated with

No associations

Rating

KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-324278