Difference between revisions of "MSAT (analysis)"

Revision as of 18:14, 9 December 2020

Analysis title

MSAT

Provider

geneXplain GmbH

Class

MSAT

Plugin

com.genexplain.tfbs (geneXplain tfbs)

Description

Motif Score Association Test (MSAT) is a tool to test for association between a motif score and a quantity of interest using generalized linear models (glms).

For each TFBS motif of specified profile, scores are calculated for promoter sequences of input genes. R's glm methodology is then applied to model the quantity of interest given with the input genes as dependent variable or response (y) and motif scores as independent variable or predictors (x):

y = f(x).

For each motif the tool reports the estimated coefficient (slope) as well as its unadjusted and adjusted p-values, where it is assumed that the results are most suitably ranked by (unadjusted or adjusted) p-values.

Parameters

• Input table - Path to input
• Species - Species
• Response - Column with response values"
• Treat response as P-values - Indicates whether response shall be treated as P-values (-log-transformed and set to a maximum if 0).
• Promoter start - Promoter start relative to TSS
• Promoter end - Promoter end relative to TSS
• Input motif profile - Profile of weight matrices
• Use high score - Use high score instead of sum of scores as sequence score.
• Use Match(TM) high score - Use Match(TM) score instead of log-odds score. (Only effective for high score).
• Output folder - Output folder for logos