ArticleGenome research2007
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
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- Article
- Colocalization analyses of genomic elements: approaches, recommendations and challenges.Bioinformatics (Oxford, England) · 2019Article
- Patterns of variation in cis-regulatory regions: examining evidence of purifying selection.BMC genomics · 2018Article
- Acetylation of VGLL4 Regulates Hippo-YAP Signaling and Postnatal Cardiac Growth.Developmental cell · 2016Article
- Unraveling heterogeneous susceptibility and the evolution of breast cancer using a systems biology approach.Genome biology · 2015Article
- Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Sequence analysis of origins of replication in the Saccharomyces cerevisiae genomes.Frontiers in microbiology · 2014Article
- Human Transcriptome and Chromatin Modifications: An ENCODE Perspective.Genomics & informatics · 2013Article
- Three distinct patterns of histone H3Y41 phosphorylation mark active genes.Cell reports · 2012Article
- Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.Genome biology · 2012Article
- Decoding the human genome.Genome research · 2012Review
- An effective statistical evaluation of ChIPseq dataset similarity.Bioinformatics (Oxford, England) · 2012Article
- A graphical modelling approach to the dissection of highly correlated transcription factor binding site profiles.PLoS computational biology · 2012Article
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Authors and funding
8 authors.
Funding
Abstract
The comprehensive inventory of functional elements in 44 human genomic regions carried out by the ENCODE Project Consortium enables for the first time a global analysis of the genomic distribution of transcriptional regulatory elements. In this study we developed an intuitive and yet powerful approach to analyze the distribution of regulatory elements found in many different ChIP-chip experiments on a 10 approximately 100-kb scale. First, we focus on the overall chromosomal distribution of regulatory elements in the ENCODE regions and show that it is highly nonuniform. We demonstrate, in fact, that regulatory elements are associated with the location of known genes. Further examination on a local, single-gene scale shows an enrichment of regulatory elements near both transcription start and end sites. Our results indicate that overall these elements are clustered into regulatory rich "islands" and poor "deserts." Next, we examine how consistent the nonuniform distribution is between different transcription factors. We perform on all the factors a multivariate analysis in the framework of a biplot, which enhances biological signals in the experiments. This groups transcription factors into sequence-specific and sequence-nonspecific clusters. Moreover, with experimental variation carefully controlled, detailed correlations show that the distribution of sites was generally reproducible for a specific factor between different laboratories and microarray platforms. Data sets associated with histone modifications have particularly strong correlations. Finally, we show how the correlations between factors change when only regulatory elements far from the transcription start sites are considered.
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