Epigenetic Tools and Resources

Tools, where would mankind be without them? The EpiGenie team decided to search out and compile a list of the best tools and databases (that require no coding knowledge) that epigenetics researchers can’t live without.

Here we go:

Epigenetic Data Browsers:

Go ahead, get your feet wet with these user friendly data browsers:

  • Epigenome Browser: For the UCSC genome browser fans.
  • VizHub: Displaying sequencing data from Roadmap Epigenomics project, powered by a local mirror of UCSC Genome Browser.
  • WashU Epigenome Browser: A new-generation genome browser for integrative visualization of genomic information. Hosts high volume of tracks from ENCODE and Roadmap Epigenomics projects, supports multiple organisms, visualizes chromatin-interaction data (e.g. Hi-C), performs gene set view, gene plot, and many others. All delivered on the web at high performance.
  • NCBI: Did you know they had and epigenomics section? Explore, view, and download genome-wide maps of DNA and histone modifications from their diverse collection of epigenomic data sets
  • Ensembl: Now featuring ENCODE.
  • GenExp: A web-based visualization tool to interactively explore a genomic database.

Epigenetic Databases:

While you’re a pioneer, you’re certainly not the first one to tread these waters. Go have a look at lifetime’s of work:

Chromatin

  • Histome: a database dedicated to displaying information about human histone variants, sites of their post-translational modifications and about various histone modifying enzymes.
  • CosBI: The histone code, dare you crack it? Learn more about CosBI from Epigenie.
  • Pscan-ChIP: a web server which scans ChIP seq genomic region data for over-representated transcription factor binding site motifs.

DNA Methylation

  • MethylomeDB: The Brain Methylome Database! This database includes genome-wide DNA methylation profiles for human and mouse brains.
  • DiseaseMeth: A web based resource focused on the aberrant methylomes of human diseases.
  • NGSmethDB: A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes. We collect NGS data from high-throughput sequencing together with bisulfite conversion of DNA from literature and public repositories, then generating high-quality chromosome methylation maps for many different tissues, pathological conditions and species.
  • MethBase: A central reference methylome database created from public BS-seq datasets. It contains hundreds of methylomes from well studied organisms. For each methylome, Methbase provides methylation level at individual sites, hypo- or hyper-methylated regions, partially methylated regions, allele-specifically methylated regions, and detailed meta data and summary statistics.

Noncoding RNA

  • miRBase: A searchable database of published miRNA sequences and annotation.
  • TarBase: The largest manually curated target database, indexing more than 65,000 miRNA-gene interactions. The database includes targets for 21 species.
  • miRNEST: An integrative collection of animal, plant, and virus microRNA data.
  • RNA22v2: Get your miRNA targeting on with an unbiased algorithim that not only considers 3′UTR binding but also 5′UTR binding.
  • NonCode:A database of all kinds of noncoding RNAs (except tRNAs and rRNAs).
  • Human lincRNA Catalog:  A unifying catalogue of previously existing annotation sources with transcripts assembled from RNA-Seq data collected from ~4 billion RNA-Seq reads across 24 tissues and cell types. Each lincRNA is characterized by a panorama of more than 30 properties, including sequence, structural, transcriptional, and orthology features.
  • miRSNP: Linking sequence to trait, check out what polymorphisms in your microRNA can do.

Other Useful Databases:

  • MpromDB: Mammalian Promoter Database.
  • cisRED: A database that holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations.

Epigenetic Data Repositories:

These house some of the ‘raw’ sources of information that databases go through:

  • GEO: The granddaddy of epigenomics data repositories. This page summarizes Roadmap Epigenomics project data that are available through the GEO repository.
  • The Epigenome Atlas: It includes human reference epigenomes and the results of their integrative and comparative analyses.
  • CEEHRC Platform: A reference epigenome project for human cells, and not the typical stem cell lines.
  • SampleBrowser: Part of NCBI’s epigenomics.
  • Galaxy: An open, web-based platform for data intensive biomedical research.
  • Classification of Human Transcription Factors: The mother list of transcription factors and their binding sites.

Epigenetic Tools for Statistical Data Analysis and Visualization:

Results are great! Now go do something with them. Use these data analysis and visualization tools to help decipher your data. Need to get a little intro into biostatistics? Check out these essentials from the bioconductor database to get you started with data that won’t analyze the easy way, or this link to show how  sometimes a little R can useful. Here are a few of the best data analysis and visualization packages out there:

  • MOABS: Bioinformatic method for detecting differential DNA methylation from bisulfite sequencing data.
  • ChAMP: call CNVs from your Infinium 450k methylation datasets and process away.
  • Minifi: Take cellular heterogeneity on your 450k arrays into account, after all variety is the spice to life.
  • DMAP: a (C-based) tool for RRBS and WGBS data, which includes a suite of statistical tools and a different investigating approach for analysing DNA methylation data and it also links any list of regions to the genome and provides gene and CpG features.  It now features a novel fragment based analysis for RRBS, which has not been shown before.
  • ZENBU: japanese for all, entire, whole, altogether. This browser lets you integrate and interact with your multiple omic data sets in a nice visual environment.
  • EpiExplorer: Import your very own data and compare it to ENCODE.
  • Podbat: A positioning database and analysis tool that incorporates data from various sources and allows detailed dissection of the entire range of chromatin modifications simultaneously. Podbat can be used to analyze, visualize, store and share epigenomics data. Also be sure to check out our coverage on Podbat.
  • MethPipe: A computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS).
  • ALEA: Lets you analyze ChIP-seq or RNA-seq data to correlate allele-specific differences with epigenomic status.
  • Homer: A novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. The art is just a bonus.
  • The MEME Suite: Motif Based Sequence Analysis Tools.
  • CTCF Insulator Database: in silico prediction for all your genomic insulation needs!
  • CENTDIST: a novel web-application for identifying co-localized transcription factors around ChIP-seq peaks. Unlike traditional motif scanning program, it does not require any user-specific parameters and the background. It automatically learns the best set of parameters for different motifs and ranks them based on the skewness of their distribution around ChIP-seq peaks.
  • ChIP-Array: A combination of ChIP-seq/chip Transcription Factor Binding Sites and gene expression platform. It takes ChIP-Array or ChIP-seq expression data together to construct a regulatory network around a Transcription Factor of interest in human, mouse, yeast, fly, and arabidopsis.
  • Regulatory Sequence Analysis Tools: detects regulatory signals in non-coding sequences.
  • CARRIE: It takes takes two condition microarray data and applies promoter analysis to infer the stimulated/repressed transcriptional regulatory network.
  • DiRE: A web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding site information. DiRE allows users to start analysis with raw microarray expression data.
  • FatiGO: Gene expression and functional profiling analysis suite.
  • oPOSSUM: Web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.
  • Melina: (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.

Sodium Bisulfite Primer Design:

When Bisulfite reduces the complexity of a sequence, it increases the complexity of it’s primer design. These programs help take the pain out of bisulfite primer design:

  • BiSearch: BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method.
  • MethPrimer: a program for designing bisulfite-conversion-based methylation PCR primers. Currently, it can design primers for two types of bisulfite PCR: 1) Methylation-Specific PCR (MSP) and 2) Bisulfite-Sequencing PCR (BSP) or Bisulfite-Restriction PCR. MethPrimer can also predict CpG islands in DNA sequences
  • Bisulfite Primer Seeker: Zymo Research’s handy online bisulfite primer design tool, designed by experts.

Got a tool you dig? Let us know about it so we can share it in the spirit of open science!