Towards Understanding the Relations Among Co-expressions, Annotations and
Co-regulations
Microarray technology provides an opportunity to view
transcriptions at genomic level under different conditions
controlled by an experiment. From an array experiment, few
hundreds of differentially expressed genes are selected and are
clustered using one of several standard algorithms. Generally, coexpressed
genes, which are members of the same cluster, are
expected to have similar function, but unfortunately it is not often
true. A functional annotation often refers to molecular function
and biological processes and there is no specific way to combine
the functional annotation when it comes to associating them with
clusters. We will show that the proposed method based on
singular value decomposition performs better than a typical
smoothing technique. Co-regulated genes are often expressed
simultaneously and are expected to have similar function. In this
paper, we will propose a systematic method to study the relations
among co-expression, co-regulation and functional annotations.
We will illustrate the method with a recent microarray
experimental conducted for identifying transcriptional targets of
integrin a6b4 for breast cancer progression.
Index Terms
Information content, gene ontology, annotation.
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