Design and analysis of ChIP-seq experiments for DNA-binding proteins. Export

@article{citeulike:3748163, abstract = {Recent progress in massively parallel sequencing platforms has enabled genome-wide characterization of DNA-associated proteins using the combination of chromatin immunoprecipitation and sequencing (ChIP-seq). Although a variety of methods exist for analysis of the established alternative ChIP microarray (ChIP-chip), few approaches have been described for processing ChIP-seq data. To fill this gap, we propose an analysis pipeline specifically designed to detect protein-binding positions with high accuracy. Using previously reported data sets for three transcription factors, we illustrate methods for improving tag alignment and correcting for background signals. We compare the sensitivity and spatial precision of three peak detection algorithms with published methods, demonstrating gains in spatial precision when an asymmetric distribution of tags on positive and negative strands is considered. We also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites.}, author = {Kharchenko, Peter V. and Tolstorukov, Michael Y. and Park, Peter J.}, citeulike-article-id = {3748163}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt.1508}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt.1508}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19029915}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19029915}, comment = {'[...] sequencing of input material is essential to properly account for the background tag distribution. Sequencing of a mock control experiment (nonspecific antibody or no antibody) may also be necessary.' ---=note-separator=--- '[...] background-driven false-positive positions are generally smaller in magnitude and begin to influence predictions as more binding positions are considered.' ---=note-separator=--- 'Background corrections have limited effect on the precision [distance of peak from motif center] of the predicted positions [...]' ---=note-separator=--- 'For the CTCF [...] predictions [...] the MTC method achieves better precision [smaller distances between peaks and motif centers] [...]' ---=note-separator=--- '[...] Poisson-based [theoretical background] model underestimates FDRs between 8- and 20-fold [...]' ---=note-separator=--- minimal saturated enrichment ratio (MSER): '[...] an experiment of given depth [number of tags] may saturate detection of the binding positions that exceed a certain tag enrichment ratio relative to the background.'}, day = {16}, doi = {10.1038/nbt.1508}, issn = {1546-1696}, journal = {Nature biotechnology}, keywords = {analysis-tool, background, benchmark, bioinformatics, chip-seq, csp, ctcf, deep-seq, experiment-planning, msp, mtc, pipeline, read-coverage, wtd, xset}, month = {December}, number = {12}, pages = {1351--1359}, posted-at = {2008-12-06 11:14:57}, priority = {0}, publisher = {Nature Publishing Group}, title = {Design and analysis of ChIP-seq experiments for DNA-binding proteins.}, url = {http://dx.doi.org/10.1038/nbt.1508}, volume = {26}, year = {2008} }

TY - JOUR ID - citeulike:3748163 L3 - citeulike-article-id:3748163 N2 - Recent progress in massively parallel sequencing platforms has enabled genome-wide characterization of DNA-associated proteins using the combination of chromatin immunoprecipitation and sequencing (ChIP-seq). Although a variety of methods exist for analysis of the established alternative ChIP microarray (ChIP-chip), few approaches have been described for processing ChIP-seq data. To fill this gap, we propose an analysis pipeline specifically designed to detect protein-binding positions with high accuracy. Using previously reported data sets for three transcription factors, we illustrate methods for improving tag alignment and correcting for background signals. We compare the sensitivity and spatial precision of three peak detection algorithms with published methods, demonstrating gains in spatial precision when an asymmetric distribution of tags on positive and negative strands is considered. We also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites. IS - 12 JF - Nature biotechnology SN - 1546-1696 EP - 1359 TI - Design and analysis of ChIP-seq experiments for DNA-binding proteins. PB - Nature Publishing Group VL - 26 SP - 1351 KW - analysis-tool KW - background KW - benchmark KW - bioinformatics KW - chip-seq KW - csp KW - ctcf KW - deep-seq KW - experiment-planning KW - msp KW - mtc KW - pipeline KW - read-coverage KW - wtd KW - xset N1 - '[...] sequencing of input material is essential to properly account for the background tag distribution. Sequencing of a mock control experiment (nonspecific antibody or no antibody) may also be necessary.' N1 - '[...] background-driven false-positive positions are generally smaller in magnitude and begin to influence predictions as more binding positions are considered.' N1 - 'Background corrections have limited effect on the precision [distance of peak from motif center] of the predicted positions [...]' N1 - 'For the CTCF [...] predictions [...] the MTC method achieves better precision [smaller distances between peaks and motif centers] [...]' N1 - '[...] Poisson-based [theoretical background] model underestimates FDRs between 8- and 20-fold [...]' N1 - minimal saturated enrichment ratio (MSER): '[...] an experiment of given depth [number of tags] may saturate detection of the binding positions that exceed a certain tag enrichment ratio relative to the background.' AU - Kharchenko, Peter AU - Tolstorukov, Michael AU - Park, Peter PY - 2008/12/16/ UR - http://dx.doi.org/10.1038/nbt.1508 ER -