A Primer on Regression Methods for Decoding cis-Regulatory Logic

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


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/PublicationReferenceLinear 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)