“ Decoding Mammalian Gene Regulatory Programs through Efficient Microarray , ChIP - chip and Sequence Analysis ”
نویسنده
چکیده
An empirical hierarchical Bayes approach was first proposed to analyze gene expression data collected from microarray experiments. Through a closed-form variance shrinkage estimator, information from multiple genes is pooled to increase the statistical power of multiple hypothesis testing. The approach also allows various types of subject matter knowledge to be incorporated conveniently. Caveats in controlling false discovery rate (FDR) will be discussed. When variance shrinkage estimator is employed, inappropriate use of permutations may result in underestimation of FDR.
منابع مشابه
Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters.
ChIP coupled with microarray provides a powerful tool to determine in vivo binding profiling of transcription factors to deduce regulatory circuitries in mammalian cells. Aiming at improving the specificity and sensitivity of such analysis, we developed a new technology called ChIP-DSL using the DNA selection and ligation (DSL) strategy, permitting robust analysis with much reduced materials co...
متن کاملW-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data
MOTIVATION Position weight matrices (PWMs) are widely used to depict the DNA binding preferences of transcription factors (TFs) in computational molecular biology and regulatory genomics. Thus, learning an accurate PWM to characterize the binding sites of a specific TF is a fundamental problem that plays an important role in modeling regulatory motifs and also in discovering the regulatory targ...
متن کاملDiscovering transcription factor regulatory targets using gene expression and binding data
MOTIVATION Identifying the target genes regulated by transcription factors (TFs) is the most basic step in understanding gene regulation. Recent advances in high-throughput sequencing technology, together with chromatin immunoprecipitation (ChIP), enable mapping TF binding sites genome wide, but it is not possible to infer function from binding alone. This is especially true in mammalian system...
متن کاملMPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data
We have developed Mammalian Promoter Database (MPromDb), a novel database that integrates gene promoters with experimentally supported annotation of transcription start sites, cis-regulatory elements, CpG islands and chromatin immunoprecipitation microarray (ChIP-chip) experimental results with intuitively designed presentation. Release 1.0 of MPromDb currently contains 36,407 promoters and fir...
متن کاملA Gibbs sampler for the identification of gene expression and network connectivity consistency
MOTIVATION Data from DNA microarrays and ChIP-chip binding assays often form the basis of transcriptional regulatory analyses. However, experimental noise in both data types combined with environmental dependence and uncorrelation between binding and regulation in ChIP-chip binding data complicate analyses that utilize these complimentary data sources. Therefore, to minimize the impact of these...
متن کامل