CEAS: cis-regulatory element annotation system

By Xuwo Ji, Wei Li, Jun S. Song, Liping Wei, X. S. Liu. Nucleic Acids Res., 2006

533 citations recorded by the source corpus.

The recent availability of high-density human genome tiling arrays enables biologists to conduct ChIP–chip experiments to locate the in vivo-binding sites of transcription factors in the human genome and explore the regulatory mechanisms. Once genomic regions enriched by transcription factor ChIP–chip are located, genome-scale downstream analyses are crucial but difficult for biologists without strong bioinformatics support. We designed and implemented the first web server to streamline the ChIP–chip downstream analyses. Given genome-scale ChIP regions, the cis-regulatory element annotation system (CEAS) retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes and identifies enriched transcription factor-binding motifs. Biologists can utilize CEAS to retrieve useful information for ChIP–chip validation, assemble important knowledge to include in their publication and generate novel hypotheses (e.g. transcription factor cooperative partner) for further study. CEAS helps the adoption of ChIP–chip in mammalian systems and provides insights towards a more comprehensive understanding of transcriptional regulatory mechanisms. The URL of the server is .

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c3c29c25113749197a53ea6842fd25e42c53885d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases (2014, background): “Some programs [12,13] have incorporated simple functions for a user to generate average profile plots at TSSs, TESs, or genebody regions, but with very limited options to customize the figures.”
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data (2010, methodology): “Several useful web applications have been developed for managing and annotating ChIP-chip data [12-14] and ChIP-seq data [14].”
The PR/SET Domain Zinc Finger Protein Prdm4 Regulates Gene Expression in Embryonic Stem Cells but Plays a Nonessential Role in the Developing Mouse Embryo (2013, methodology): “seq peaks compared to gene annotations was determined using CEAS (47).”
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. (2008, unknown): “…H3K27me1, me2, me3 (07-448, 07-449, and 07-452 from Upstate Biotechnology Inc.) (Barski et al., 2007; Mikkelsen et al., 2007; Vakoc et al., 2006 Genomic distribution of binding sites identified by ChIP-chip was performed using cis-regulatory element annotation system (CEAS) (Ji et al., 2006).”
seqMINER: an integrated ChIP-seq data interpretation platform (2010, background): “…analysis pipelines, have been proposed that allow: annotation of genomic features present in the neighbourhood of the relevant enrichment signals (5–7), detection and de novo deﬁnition of consensus DNA motifs (6), cross and compare information from distinct datasets (8) and comprehensive…”
Cistrome: an integrative platform for transcriptional regulation studies (2011, methodology): “Therefore, a set of tools from the CEAS (Cis-regulatory Element Annotation System) [23] package, including SitePro, GCA (Gene Centered Annotation), Peak2Gene and the CEAS main program, has been deployed in the Cistrome web interface.”
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data (2011, background): “Most of the tools published for the analysis of ChIP-Seq data focus on punctuated signals (Fejes et al., 2008; Nix et al., 2008; Park, 2009; Pepke et al., 2009; Zhang et al., 2008), with only few methods devoted to analyse broad signals (Shin et al., 2009; Zang et al., 2009).”