Clustering of gene expression data using a local shape-based similarity measure.
BACKGROUND
Microarray technology enables the study of gene expression in large scale. The application of methods for data analysis then allows for grouping genes that show a similar expression profile and that are thus likely to be co-regulated. A relationship among genes at the biological level often presents itself by locally similar and potentially time-shifted patterns in their expression profiles.


RESULTS
Here, we propose a new method (CLARITY; Clustering with Local shApe-based similaRITY) for the analysis of microarray time course experiments that uses a local shape-based similarity measure based on Spearman rank correlation. This measure does not require a normalization of the expression data and is comparably robust towards noise. It is also able to detect similar and even time-shifted sub-profiles. To this end, we implemented an approach motivated by the BLAST algorithm for sequence alignment. We used CLARITY to cluster the times series of gene expression data during the mitotic cell cycle of the yeast Saccharomyces cerevisiae. The obtained clusters were related to the MIPS functional classification to assess their biological significance. We found that several clusters were significantly enriched with genes that share similar or related functions.
Balasubramaniyan
Rajarajeswari
R
Max-Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions Karl-von-Frisch-Strasse, 35043 Marburg, Germany.
Hüllermeier
Eyke
E
Weskamp
Nils
N
Kämper
Jörg
J
D000465:Algorithms; D002453:Cell Cycle / Q000502:physiology; D016000:Cluster Analysis; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal / Q000502:physiology*; D008954:Models, Biological; D010363:Pattern Recognition, Automated / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*
D029701:Saccharomyces cerevisiae Proteins