Welcome to MAnorm Web Toolkit

What is MAnorm?

MAnorm is a robust model for quantitative comparison of ChIP-Seq data sets of TFs (transcription factors) or epigenetic modifications and you can use it for:

• Normalization of two ChIP-seq samples
• Quantitative comparison (differential analysis) of two ChIP-seq samples
• Evaluating the overlap enrichment of the protein binding sites (peaks)
• Elucidating underlying mechanisms of cell-type specific gene regulation

How MAnorm works?

MAnorm uses common peaks of two samples as a reference to build the rescaling model for normalization, which is based on the empirical assumption that if a chromatin-associated protein has a substantial number of peaks shared in two conditions, the binding at these common regions will tend to be determined by similar mechanisms, and thus should exhibit similar global binding intensities across samples. The observed differences on common peaks are presumed to reflect the scaling relationship of ChIP-Seq signals between two samples, which can be applied to all peaks.

The normalized M value given by MAnorm was used as a quantitative measure of differential binding in each peak region between two samples, with peak regions associated with larger absolute M values exhibiting greater binding differences between two samples.

MAnorm is developed in Python with a command line interface, you can use it on Linux and macOS platforms. Basically, it requires a ChIP-seq peak file generated by some peak caller and a sequencing read file for each sample under comparison. MAnorm supports multiple commonly used input formats, including BED/MACS/MACS2/narrowPeak formats for peak files and BED/BEDPE/SAM/BAM formats for sequencing read files.