# The MEME Suite

## Motif-based sequence analysis tools

## CisMapper Tutorial

### What CisMapper does

### Typical CisMapper applications

- Predicting which genes are regulated by a particular transcription factor (TF) using ChIP-seq peaks for that TF.
- Predicting which ChIP-seq peak corresponds to the TF binding to regulate a particular gene.

### How CisMapper works

CisMapper uses histone modification and gene expression data for a panel of 'tissues'. It computes the level of each histone modification for which it has data at each of the genomic loci (typically ChIP-seq peaks) that you provide. It then for each locus, it computes the Pearson correlation between a histone modification at the locus and each gene whose transcription start site (TSS) is located within a specified maximum distance from the locus. CisMapper reports a score for each locus-TSS-histone trio. The score is the p-value of the Pearson correlation coefficient. CisMapper also computes a single score for each gene that is the mininum score across all potential regulatory links (and histone modifications), adjusted for multiple testing.

### Loci

You provide a set of genomic loci to CisMapper via a 'locus file' in BED format. Each line in the locus file specifies a single locus specified as three fields separated by tabs: <chrom> <chromStart> <chromEnd>. Any additional fields on each line are ignored by CisMapper, as are comment lines, which must start with the '#' character.

### CisMapper Web Server Histone + Expression Panels

You must choose a panel for the exact genome release (assembly) used by your loci file for CisMapper to work correctly. If a panel does not exist for your genome release, you may be able to use the LiftOver tool to convert your loci to the correct coordinates.

### Creating your own Histone + Expression Panels

Under construction...

### FAQ

- Under construction...