NDLI: Microarray Time Course Experiments: Finding Profiles

Content Provider	ACM Digital Library
Author	Irigoien, Itziar Vives, Sergi Arenas, Concepcion
Abstract	Time course studies with microarray techniques and experimental replicates are very useful in biomedical research. We present, in replicate experiments, an alternative approach to select and cluster genes according to a new measure for association between genes. First, the procedure normalizes and standardizes the expression profile of each gene, and then, identifies scaling parameters that will further minimize the distance between replicates of the same gene. Then, the procedure filters out genes with a flat profile, detects differences between replicates, and separates genes without significant differences from the rest. For this last group of genes, we define a mean profile for each gene and use it to compute the distance between two genes. Next, a hierarchical clustering procedure is proposed, a statistic is computed for each cluster to determine its compactness, and the total number of classes is determined. For the rest of the genes, those with significant differences between replicates, the procedure detects where the differences between replicates lie, and assigns each gene to the best fitting previously identified profile or defines a new profile. We illustrate this new procedure using simulated data and a representative data set arising from a microarray experiment with replication, and report interesting results.
Starting Page	464
Ending Page	475
Page Count	12
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2009.79
Volume Number	8
Issue Number	2
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2011-03-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Cluster analysis, typical unit, gene profile, time course experiment, replicate.
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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