CEAS: cis-regulatory element annotation system
Abstract
Unlabelled We present a tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq data. This stand-alone extension of our web application CEAS (cis-regulatory element annotation system) provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene bodies or exons, and infers the genes most likely to be regulated by the binding factor under study. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic regions, particularly allowing observation of continuous and broad ChIP enrichment that might be too subtle to detect from ChIP peaks alone. Availability The CEAS Python package is publicly available at http://liulab.dfci.harvard.edu/CEAS.
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HNF4A and FOXA2 coenrichment sites, like the majority of all HNF4A and FOXA2 sites, are frequently located within distal intergenic regions.
“Sites of coenrichment, like the majority of all HNF4A and FOXA2 sites, were frequently found within distal intergenic regions (Figure S1; Shin et al., 2009).”
From Hippo Signaling Influences HNF4A and FOXA2 Enhancer Switching during Hepatocyte Differentiation (2014) · cites this paper as Shin et al., 2009
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- Authors
- Shin, H., Liu, T., Manrai, A. K., & Liu, X. S.
- Affiliations
- Harvard–MIT Division of Health Sciences and Technology (US)
- Corresponding author
- Liu, X. Shirley
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-08-18
- Volume
- 25
- Issue
- 19
- Pages
- 2605-2606
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2123460634
- Cited by
- 461
- References
- 1
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 18 · 2023: 9 · 2022: 26 · 2021: 23 · 2020: 19 · 2019: 38 · 2018: 37 · 2017: 41 · 2016: 28 · 2015: 47 · 2014: 41 · 2013: 49 · 2012: 27
- FWCI
- 9.38
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- cis-regulatory elements, protein-DNA interactions, ChIP-chip, ChIP-seq, promoter binding, signal visualization, cavity-enhanced absorption spectroscopy
- MeSH terms
- Regulatory Sequences, Nucleic Acid, Software, Genome, Computational Biology, Databases, Genetic
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