Difference between revisions of "MEALR (tracks) (analysis)"

Latest revision as of 18:14, 9 December 2020

Analysis title

MEALR (tracks)

Provider

geneXplain GmbH

Class

MEALR

Plugin

com.genexplain.analyses (geneXplain analyses)

[edit] MEALR - Motif Enrichment Analysis by Logistic Regression

[edit] Parameters

• Yes set - Study track / Track with intervals of interest
• No set - Background track / Track of non-bound intervals
• Sequence source - Choose a deployed sequence source from the pull-down list. Selecting Custom enables setting of a custom sequence collection
• Input motif profile - Profile of weight matrices
• Output path - Path in workspace to store output table

[edit] Output

The output contains two columns. The ID column contains identifiers of motifs to which MEALR assigned a positive coefficient. The coefficients are listed in the column named Coefficient.

[edit] Description

MEALR searches for a combination of transcription factor binding motifs that discriminate between a positive (Yes) and a negative (No) sequence set. The Yes sequences are the sequences of interest, e.g. as identified in a ChIP-seq experiment.

Sparse logistic regression assigns non-zero coefficients to only a small subset of motifs specified by an input profile. The coefficients indicate the importance of a motif for discrimination. Hence, MEALR differs from other site enrichment tools by choosing an optimal subset of motifs from a possibly large motif database.

Currently, the output contains only the set of motifs with positive coefficients. The larger the coefficient, the more important the corresponding motif was for discriminating between Yes and No sequences.