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

@article{citeulike:5407395, 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 transcription starting sites on the DBTSS library, while many other newly identified sites have a high chance to be real binding sites based on a high positive predictive value of DES. We also showed the superior performance of DES compared with other commonly used methods for detecting actual protein binding sites. Contact: tspark@snu.ac.kr; jaeklee@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btp471}, author = {Kim, Youngchul and Bekiranov, Stefan and Lee, Jae K. and Park, Taesung}, citeulike-article-id = {5407395}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp471}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/19/2486.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/19/2486.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19667080}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19667080}, day = {1}, doi = {10.1093/bioinformatics/btp471}, journal = {Bioinformatics}, keywords = {chip-chip}, month = {October}, number = {19}, pages = {2486--2491}, posted-at = {2009-09-28 19:25:59}, priority = {2}, title = {Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication}, url = {http://dx.doi.org/10.1093/bioinformatics/btp471}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:5407395 L3 - citeulike-article-id:5407395 N2 - 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 transcription starting sites on the DBTSS library, while many other newly identified sites have a high chance to be real binding sites based on a high positive predictive value of DES. We also showed the superior performance of DES compared with other commonly used methods for detecting actual protein binding sites. Contact: tspark@snu.ac.kr; jaeklee@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btp471 IS - 19 JF - Bioinformatics EP - 2491 TI - Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication VL - 25 SP - 2486 KW - chip-chip AU - Kim, Youngchul AU - Bekiranov, Stefan AU - Lee, Jae AU - Park, Taesung PY - 2009/10/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp471 ER -