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
7 ACTB genes and 13 randomly picked genes.
View HTML7 ACTB genes and 13 randomly picked genes.
View HTML7 ACTB genes and 13 randomly picked genes.
View HTML7 ACTB input sequences.
View HTML7 ACTB input sequences.
View HTML6 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
Input Matrix: 46 regulatory regions
View HTMLInput 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
Input Matrix: 46 regulatory regions
View HTMLInput 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
Modules detected: GA vs Toucan
View HTMLModules detected: GA vs Toucan
View HTMLDatasets after stringent settings for MotifScanner
MotifScanner parameters: prior probability: 0.1; background model: EPD human-3rd order
Modules detected: GA vs Toucan
View HTMLModules detected: GA vs Toucan
View HTML