Paul Perco (1,2,3), Alexander Kainz (2), Gert Mayer (3), Arno Lukas (1,4), Rainer Oberbauer (2), and Bernd Mayer(1,4)
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
![Data Set 2.1: Data Set 2.1:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_Data-Set-2.1.gif)
7 ACTB genes and 13 randomly picked genes.
View HTML![Data Set 2.2: Data Set 2.2:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_Data-Set-2.2.gif)
7 ACTB genes and 13 randomly picked genes.
View HTML![Data Set 2.3: Data Set 2.3:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_Data-Set-2.3.gif)
7 ACTB genes and 13 randomly picked genes.
View HTML![CAAT Box: CAAT Box:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_CAAT-Box.gif)
7 ACTB input sequences.
View HTML![SRF Motif: SRF Motif:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_SRF-Motif.gif)
7 ACTB input sequences.
View HTML![mTATA Box: mTATA Box:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_mTATA-Box.gif)
6 ACTB input sequences.
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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
![Data Set 3.1: Data Set 3.1:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_Data-Set-3.1.jpg)
Input Matrix: 46 regulatory regions
View HTML![Data Set 3.2: Data Set 3.2:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_Data-Set-3.2.jpg)
Input Matrix: 46 regulatory regions plus 40 random sequences
View HTMLDatasets after stringent settings for MotifScanner
MotifScanner parameters: prior probability: 0.1; background model: EPD human-3rd order
![Data Set 3.3: Data Set 3.3:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_Data-Set-3.3.jpg)
Input Matrix: 46 regulatory regions
View HTML![Data Set 3.4: Data Set 3.4:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_Data-Set-3.4.jpg)
Input Matrix: 46 regulatory regions plus 40 random sequences
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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
![Data Set 3.1: Data Set 3.1:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_3_Data-Set-3.1.gif)
Modules detected: GA vs Toucan
View HTML![Data Set 3.2: Data Set 3.2:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_3_Data-Set-3.2.gif)
Modules detected: GA vs Toucan
View HTMLDatasets after stringent settings for MotifScanner
MotifScanner parameters: prior probability: 0.1; background model: EPD human-3rd order
![Data Set 3.3: Data Set 3.3:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_3_Data-Set-3.3.gif)
Modules detected: GA vs Toucan
View HTML![Data Set 3.4: Data Set 3.4:](https://www.meduniwien.ac.at/nephrogene/wp-content/uploads/2013/03/51_3_Data-Set-3.4.gif)
Modules detected: GA vs Toucan
View HTML