Data resources

  • EPD: The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.
  • UCNEbase is a database providing information on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs) in multiple vertebrate species.
  • HTPSELEX is a database containing sets of in vitro selected transcription factor binding site sequences obtained with SELEX and a high-throughput SELEX method.
  • MGA: The Mass Genome annotation (MGA) repository contains functional genomics data in a standardized format.
  • TromER: A web interface to human transcripts from the transcriptome analyser (TROMER) project (also viewable at the UCSC genome browser, see tracks “SIB Genes” and “SIB Alt-Splicing”).
  • CleanEx provides access to public gene expression data via unique approved gene symbols. It represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.

Web servers

  • ChIP-Seq: The ChIP-Seq Web Server provides access to a set of useful tools performing common ChIP-Seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions.
  • SSA: Web access to the Signal Search Analysis (SSA) software package useful for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site, e.g. a transcription or translation initiation site.
  • PWMTools: A collection of position weight matrix (PWM)-centric web-based tools, including PWMScan allowing for whole genome scans with a PWM.
  • ZFN-Site: Based on the TagScan tool, this application is intended to search genomes for specific target sites and off-target sites of DNA-binding proteins such zinc finger proteins (ZFPs), zinc finger nucleases (ZFNs) and modified homing endonucleases.
  • Tagger is a tool which allows searching fixed-size sequence tags (or sequence branches) against entire genomes or mRNA reference sequence databases.
  • MADAP is a 1D clustering tool for genomic features such as transcription start sites. It performs a task similar to that of a ChIP-seq peak finder but uses a different algorithm.

Open source software

  • ChIP-Seq tools: The tools installed at the back-end of the ChIP-Seq server, a collection of command-line programs performing common tasks in ChIP-seq data analysis.
  • SibRNAfold: A “sparsified” version of Vienna RNAfold, which is up to 30 times faster than the original program while guaranteed to produce identical results.

More information about our services and resources

Resources1

UCSC genome browser view of the human MGMT promoter. The EPD-supplied tracks show the distribution of transcription start sites at single-base resolution, the abundances of promoter-specific histone variants H3K4me3 and H2AZ, the methylation status of the DNA and the localization of RNA polymerase II on the DNA. Note that the DNA methylation status of this promoter serves as a predictive marker for therapy choice in certain types of cancer.

 

 

 

 

 

 

 

 

 

Resources2

Input form and results page of the PWMScan server. Upper right: Input form. Centre left: Sequence logo of the position weight matrix entered. Bottom: Results page with action buttons for saving the match list, for extracting surrounding DNA sequences or sending the results to another web application.