A Primer on Regression Methods for Decoding cis-Regulatory Logic

Debopriya Das¹, Matteo Pellegrini², Joe W. Gray^1,3

¹Life Sciences Division, Ernest O. Lawrence Berkeley National Laboratory. Berkeley, California, United States of America.
²Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America.
³Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America.

**A Catalog of Currently Available Regression Tools for *cis*-Regulatory Element Identification**
Software/Publication	Reference	Linear or Nonlinear?	Degenerate or Nondegenerate Motifs?	Identifies Target Genes?	Web Site for Download
REDUCE	Bussemaker et al. (2001)	Linear	Nondegenerate	N	http://bussemaker.bio.columbia.edu:8080/reduce/
MODEM	Wang et al. (2005)	Linear	Weakly degenerate	Y	http://wanglab.ucsd.edu/
Pham et al.*	Pham et al. (2007)	Nonlinear (sigmoidal)	-	Y	NA
MARSMotif	Das et al. (2004)	Nonlinear (MARS)	Nondegenerate or weakly degenerate	N	http://rulai.cshl.edu/licensing/index1.htm
MARSMotif-M	Das et al. (2006)	Nonlinear (Linear spline/ MARS)	Degenerate	Y	http://rulai.cshl.edu/licensing/index1.htm
MotifRegressor	Conlon et al. (2003)	Linear	Degenerate	N	http://www.math.umass.edu/~conlon/mr.html
Keles et al.	Keles et al. (2002)	Linear	Nondegenerate	N	Available upon request
Motif Expression Decomposition (MED)	Nguyen et al. (2006)	Nonlinear	Degenerate	Y	NA
Inferelator*	Bonneau et al. (2006)	Nonlinear (LARS/LASSO)	-	Y	http://err.bio.nyu.edu/inferelator/
RSIR	Zhong et al. (2005)	Nonlinear (SIR)	Degenerate	N	Available upon request
MatrixREDUCE	Foat et al. (2006)	Linear	Degenerate	N	http://bussemaker.bio.columbia.edu/software/MatrixREDUCE/
TRANSMODIS	Yu et al. (2008)	Linear	Degenerate	Y	http://haedi.ucsd.edu/
Segal et al.	Segal et al. (2008)	Nonlinear (sigmoidal)	Degenerate	Y	NA
Prego	Tanay et al. (2006)	Nonparametric	Degenerate	Y	http://uqbar.rockefeller.edu/~atanay/prego/
MA-Networker*	Gao et al. (2004)	Linear	-	Y	http://bussemaker.bio.columbia.edu/tools/
fREDUCE	Wu et al. (2007)	Linear	Degenerate	N	http://genome3.ucsf.edu:8080/freduce/
SCAD	Wang et al. (2007)	Nonlinear in time, linear in motif parameters	Degenerate	N	NA
MotifScorer	Brilli et al. (2007)	Linear (Partial least squares)	Degenerate	N	Available upon request
Minz et al.	Minz et al. (2008)	Nonlinear (FOS)	Nondegenerate	N	NA
Zhang et al.	Zhang et al. (2008)	Nonlinear	Nondegenerate	N	http://www-stat.stanford.edu/~nzhang/ZSW/

*	The tools marked with an asterisk were not originally used with cis-regulatory motifs as input, but can be easily adapted for this purpose.
+	NA indicates not available (we did not find this reported in the original paper or via Web search)

A Primer on Regression Methods for Decoding cis-Regulatory Logic

Debopriya Das1, Matteo Pellegrini2, Joe W. Gray1,3

Debopriya Das¹, Matteo Pellegrini², Joe W. Gray^1,3