Gene Regulation

Eukaryotic gene regulatory mechanisms that induce or repress the expression of a gene include structural and chemical changes to the chromatin and the DNA, binding of proteins to specific DNA elements, or mechanisms that modulate translation of mRNA.

Epigenetic mechanisms regulate many important biological processes during normal growth and development, and these mechanisms are deregulated in diseases such as cancer and diabetes.

Several techniques for characterizing the numerous regulatory and epigenomic modifications have been coupled with massively parallel sequencing strategies (NGS methods) to understand gene regulation. These include methods for characterizing interactions between protein, DNA, and RNA to survey transcription factor binding sites and histone modifications (ChIP-Seq), understand DNA methylation (Whole-Genome Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS), Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq), understand DNA accessibility changes within the chromatin (ATAC-seq, FAIRE-seq, DNase-seq), chromatin conformation capture methods (3C, 4C, 5C, Hi-C), nucleosome occupancy and positioning (MNase-Seq, CC-Seq and ChIP-Seq), etc.

Explore and integrate results from your favorite peak callers by simply uploading your peaks, filter and annotate peaks, search over and subset your data, perform statistical analyses and visualize the data.

Tools

bowtie2	Ultra-fast, sensitive gapped, short-read aligner.
bwa	Software package for mapping low-divergent sequences against a large reference genome.
MACS2	Model-based Analysis of ChIP-Seq (MACS), for identifying transcription factor binding sites.
DFilter	Generalized signal detection tool for analyzing NGS data by using ROC-AUC maximizing linear filter for detecting peaks.
SICER	Spatial Clustering for Identification of ChIP-Enriched Regions for epigenomic data.
PeakRanger	Multi-purpose software suite for analyzing ChIP-seq data - estimate noise, calculate library complexity, call narrow and broad peaks, generate coverage files, HTML-based annotation reports, etc. Tools include Ranger, BCP, CCAT, etc.
GEM	High resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data.
MEME Suite	Motif-based sequence analysis tools for motif discovery, motif enrichment analysis, motif scanning, motif comparison, etc.
HOMER	Hypergeometric Optimization of Motif EnRichment) is a suite of tools for motif discovery and for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.
bedtools	Tool to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
deepTools	Suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, MNase-seq, etc.
BS-Seeker2	Accurate, versatile, ultra-fast pipeline for processing bisulfite-converted reads.
Bismark	A flexible aligner and methylation caller for Bisulfite-Seq applications.
BSMAP	Whole genome bisulfite sequence mapping program.

File types

Visual analytics

HeatmapVisualize signal intensities of epigenomic markers across tissue types or conditions, and expresses similarities in genes.

Venn diagramCompare peak lists across various epigenomic markers and tissue types.

Volcano plotPlot differentially methylated genes and regions.

Principal Component Analysis (PCA)Reduce dimension of data, filter noise, visualize similarities between the biological samples and relate to experimental conditions.

Sequence motifDiscover and analyze sequence motifs representing DNA binding sites, protein interaction domains, etc.

Genome browserOverlay various epigenomic signals with expression data and reference annotation.

NetworkUnderstand gene regulation integrating expression with TF binding data, and other interaction data.