Detection of coregulation in differential gene expression profiles.

Return

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:

7 ACTB genes and 13 randomly picked genes.

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Data Set 2.2:
Data Set 2.2:

7 ACTB genes and 13 randomly picked genes.

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Data Set 2.3:
Data Set 2.3:

7 ACTB genes and 13 randomly picked genes.

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CAAT Box:
CAAT Box:

7 ACTB input sequences.

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SRF Motif:
SRF Motif:

7 ACTB input sequences.

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mTATA Box:
mTATA Box:

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:

Input Matrix: 46 regulatory regions

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Data Set 3.2:
Data Set 3.2:

Input Matrix: 46 regulatory regions plus 40 random sequences

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Datasets 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:

Input Matrix: 46 regulatory regions

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Data Set 3.4:
Data Set 3.4:

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:

Modules detected: GA vs Toucan

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Data Set 3.2:
Data Set 3.2:

Modules detected: GA vs Toucan

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Datasets 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:

Modules detected: GA vs Toucan

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Data Set 3.4:
Data Set 3.4:

Modules detected: GA vs Toucan

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SCIENTIFIC COLLABORATIONS