Supplemental Data

Detection of coregulation in differential gene expression profiles

Paul Perco1,2,3, Alexander Kainz2, Gert Mayer3, Arno Lukas1,4, Rainer Oberbauer2, and Bernd Mayer1,4

1 - Institute for Biomolecular Structural Chemistry, University of Vienna, Campus Vienna Biocenter 6, 1030 Vienna, AUSTRIA
2 - Department of Nephrology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, AUSTRIA
3 - Department of Nephrology, University of Innsbruck, Anichstrasse 35, 6020 Innsbruck, AUSTRIA
4 - emergentec biodevelopment, Rathausstrasse 5/3, 1010 Vienna, AUSTRIA

Implementation and Results

2. Biological data sets - 2.a. Actin beta (ACTB)

3 Promoter sequence sets
Dataset 1

Data Set 2.1

7 ACTB genes and 13 randomly picked genes

 Dataset 2

Data Set 2.2

7 ACTB genes and 13 randomly picked genes

 Dataset 3

Data Set 2.3

7 ACTB genes and 13 randomly picked genes
3 Promoter motifs - Sequence logos
CAAT Box

CAAT Box

7 ACTB input sequences

 SRF Motif

SRF Motif

7 ACTB input sequences

 mTATA Box

mTATA Box

6 ACTB input sequences

2. Biological data sets - 2.b. Muscle-specific genes

JASPAR matrices used in the analysis
Regulatory regions which confer muscle-specific gene expression
Datasets after less stringent settings for MotifScanner
MotifScanner parameters:
prior probability: 0.2; background model: EPD human-1st order
Dataset 1

Data Set 3.1

Input Matrix:
46 regulatory regions

 Dataset 2

Data Set 3.2

Input Matrix:
46 regulatory regions plus 40 random sequences
Datasets after stringent settings for MotifScanner
MotifScanner parameters:
prior probability: 0.1; background model: EPD human-3rd order
Dataset 1

Data Set 3.3

Input Matrix:
46 regulatory regions

 Dataset 2

Data Set 3.4

Input Matrix:
46 regulatory regions plus 40 random sequences

3. Comparison to other routines - 3.a. Toucan ModuleSearcher (genetic algorithm approach)

Datasets after less stringent settings for MotifScanner
MotifScanner parameters:
prior probability: 0.2; background model: EPD human-1st order
Comparison to Toucan

Data Set 3.1

Modules detected:
GA vs Toucan

 Comparison to Toucan

Data Set 3.2

Modules detected:
GA vs Toucan
Datasets after stringent settings for MotifScanner
MotifScanner parameters:
prior probability: 0.1; background model: EPD human-3rd order
Comparison to Toucan

Data Set 3.3

Modules detected:
GA vs Toucan

 Comparison to Toucan

Data Set 3.4

Modules detected:
GA vs Toucan