Basic Introduction

Method

We provide a flexible framework to perform operations related to motif analyses. Currently, the following analyses are available:
Motif Matching: Matches a set of transcription factor motifs found on the main repositories (such as Jaspar, Uniprobe and Hocomoco) against a set of genomic regions of interest.
Motif Enrichment: Performs Fisher’s exact test in order to verify if a set of genomic regions are enriched for particular transcription factors.

Installation

You can follow the general installation instructions for the RGT suite, which will automatically install the MotifAnalysis tool with all its dependencies.

After that, you must setup your RGT Data folder, unless you have already done it.

Specifically for Motif Analysis, you also need to create the Weblogos in the RGT Data folder, otherwise they will be missing from the enrichment files. More details here, but the simple command is (within the rgtdata folder):

python setupLogoData --all

Further installation instructions, including installation without pip, are found here.

Tutorial

Full-site Test

Download here. Execute the following commands in order to perform a motif matching followed by motif enrichment:

cd RGT_MotifAnalysis_FullSiteTest
rgt-motifanalysis matching --input-files input/regions_K562.bed input/background.bed 
rgt-motifanalysis enrichment input/background.bed input/regions_K562.bed

In the enrichment step, the order of the bed files matters. The background must always come first.

You can also reduce the amount of motifs used via the –filter parameter:

rgt-motifanalysis matching --filter "species:sapiens;name:EG" [other arguments..]
rgt-motifanalysis enrichment --filter "species:sapiens;name:EG" [other arguments..]

This will restrict the search to only the motifs with the string “EG” in their name (by default, the search is inexact; use –filter-type to explore different modes) and whose “species” metadata contains the “sapiens” string.

See the help file for all the available keys:

rgt-motifanalysis matching --help

You should also look into the metadata files – read here for more information.

Promoter Test

Download here. Execute the following commands in order to perform a motif matching followed by motif enrichment:

cd RGT_MotifAnalysis_PromoterTest
rgt-motifanalysis matching --target-genes input/genes.txt --input-files input/background.bed
rgt-motifanalysis enrichment input/background.bed match/target_regions.bed

In the enrichment step, the order of the bed files matters. The background must always come first.

Gene association Test

Download here. Execute the following commands in order to perform a motif matching followed by motif enrichment:

cd RGT_MotifAnalysis_GeneAssocTest
rgt-motifanalysis matching --input-matrix input_matrix.txt --rand-proportion 10
rgt-motifanalysis enrichment --input-matrix input_matrix.txt match/random_regions.bed

The matching command will read the experimental matrix, which specifies the PATH to the genomic regions and the genes to make an association test on. It also creates a background made of random regions of size 10 times the biggest genomic region in input. It might take between 10 and 30 minutes to run. It if is taking too long, use --rand-proportion 1.

The enrichment command will calculate the enrichment statistics for the all the input regions over the random background. This step should take about 5 minutes to complete.

Further usage instructions are found here.