Gene Regulation – Teif Lab

Chromatin modifications analysis

*Also have a look at related databases of nucleosome positioning and DNA-protein binding.

**The list below is focused on advanced histone modifications analysis. General-purpose peak calling tools such as MACS or SICER are not included below but also highly recommended.

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:

(Newest entries are added at the top)

EpiFactors contains information on 815 proteins, including 95 histones and protamines. It includes expressions values across several samples, in particular a collection of 458 human primary cell samples (for approximately 200 cell types, in many cases from three individual donors), covering most mammalian cell steady states, 255 different cancer cell lines (representing approximately 150 cancer subtypes) and 134 human postmortem tissues. Expression values were obtained by the FANTOM5 consortium using Cap Analysis of Gene Expression technique. EpiFactors also contains information on 69 protein complexes that are involved in epigenetic regulation. Described here.

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.

H3 methylation, H2A.Z, CTCF & Pol II occupancies (Barski et al., 2007)

H3 actetylation (Wang et al., 2008)

CREMOFAC contains 64 types of remodeling factors from 49 different organisms reported in literature (26.10.2010)