Epigenetic modifications data and tools
Software for analysis/modeling of epigenetic modifications:
dPCA identifies differential protein-DNA interactions between two biological conditions. dPCA integrates unsupervised pattern discovery, dimension reduction, and statistical inference into a single statistical framework. For each pattern, it detects and prioritizes differential genomic loci by comparing the between-condition differences with the within-condition variation among replicate samples. dPCA is part of CisGenome project. Currently, it can be run as a command line program. The authors plan incorporating it into CisGenome GUI in the future.
ChIP-PED is designed to enhance the analysis of ChIP-chip and ChIP-seq (ChIPx) data. Given the target genes of a TF in one or more cell types, ChIP-PED searches for new biological systems potentially enriched with regulatory activity of the TF by superimposing ChIPx data on large amounts of Publicly available human and mouse gene Expression Data from a diverse collection of biological systems. This allows users to extend the scope of their ChIPx data to possibly novel biological systems without performing additional costly and time-consuming ChIPx experiments.
ISMARA is an online tool that models genome-wide expression data, or any other quantitative signal along the genome, in terms of the local occurrence of computationally predicted regulatory sites for transcription factors (TFs) and micro-RNAS (miRNAs).
Histone and DNA post-translational modification databases:
EpiExplorer is a web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborous preprocessing.
A database of human histones, their post-translational modifications and modifying enzymes
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. Users can analyze their own data by uploading mapped sequence tags in various formats, including BED and BAM. The server also provides access to hundreds of publicly available data sets such as ChIP-seq data, RNA-seq data (i.e. CAGE), DNA-methylation data, sequence annotations (promoters, polyA-sites, etc.), and sequence-derived features (CpG, phastCons scores).
The browser currently hosts Human Epigenome Atlas data produced by the Roadmap Epigenomics project, but its use of advanced, multi-resolution data formats and its user-friendly interface make it possible for investigators to upload and visualize their own data as custom tracks.
- NCBI Epigenomics Sample Browser - This seems to be currently the most comprehensive collection.
- HHMD - Human Histone Modification Database (data sources include ENCODE, Zhao lab and some others)
- Data from Zhao Lab (NIH) - Genome-wide mapping of histone H3 modifications in human CD4+ T cells:
- Data from Young Lab (MIT) - Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast (Pokholok et al., 2005)
- HistoneHits - phenotypes for systematic collections of histone mutants
- MethDB - the database for DNA methylation and environmental epigenetic effects
- EpiGRAPH - software for advanced (epi-) genome analysis and prediction
- CREMOFAC - A web-database of chromatin remodeling factors
CREMOFAC contains 64 types of remodeling factors from 49 different organisms reported in literature (26.10.2010)
- ChromatinDB - visualizing histone modification data (last update in 2007?)
- Also have a look at the Wikipedia page with the list of databases