Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication.

ABSTRACT:

Motivation

ChIP-chip has been widely used for various genome-wide biological investigations. Given the small number of replicates (typically two to three) per biological sample, methods of analysis that control the variance are desirable but in short supply. We propose a double error shrinkage (DES) method by using moving average statistics based on local-pooled error estimates which effectively control both heterogeneous error variances and correlation structures of an extremely large number of individual probes on tiling arrays.

Results

Applying DES to ChIP-chip tiling array study for discovering genome-wide protein-binding sites, we identified 8400 target regions that include highly likely TFIID binding sites. About 33% of these were well matched with the known transcript

SUBMITTER: Kim Y 

PROVIDER: S-EPMC2800349 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature