Title: Microarray Evaluation for
1Microarray Evaluation for Gene Regulation
Analysis
Dr. Martin Seifert Genomatix Software
GmbH Landsberger Strasse 6, D-80339
München http//www.genomatix.de
2Microarrays today
?
Microarray experiment
Cell
3Methods for microarray data analysis
Literature analysis
Statistic analysis
Cellular processes
Sequence analysis (Genome annotation and promoter
analysis)
4PDGF Intro
A real life example
5Technology
Analysis of promoter sequences/ database scans
Promoter source for functional promoter analysis
Automatic evaluation of gene relationships
6Analysis Strategy
Analysis strategy
7Methods for microarray data analysis
Literature analysis
Statistic analysis
Cellular processes
Sequence analysis
8Cluster Analysis
hours PDGF induction
9Biology 1 subtitle
Workflow
Literature analysis
Statistic analysis
Cellular processes
Sequence analysis
10Gene Cluster
BiblioSphere Large Cluster Query
11Knowlege driven sub-clustering
highest z-score
12Knowlege driven sub-clustering
13Gene group analysis
14Knowlege driven sub-clustering
Bibliosphere on sentence level at least 4
co-citations with input genes
15Experimental verification
16Genomics subtitle
Workflow
Literature analysis
Statistic analysis
Cellular processes
Sequence analysis
17Sequence analysis
Literature analysis
18Sequence analysis
Comparative analysis of promoters within one
species -gt co-regulation
Comparative genomics of promoters -gt phylogenetic
conservation
19Intra-genomic approach
20Regulatory genome annotation
21Regulatory genome annotation
22Regulatory genome annotation
23Regulatory genome annotation
24Analysis of promoter organization
25Analysis of promoter organization
Genes sharing framework DHCR7, EBP, HMGCS1
26Analysis of promoter organization
27Beyond the microarray
framework
28Results of database search
Framework of hits in human promoters steroid biosynthesis z-score
EBOX-ECAT-ZBPF 10 3 13.55
29Model modification
30Beyond the microarray
framework with modified distance variability
31Results of database search
Framework of hits in human promoters four categories related to steroid metabolism z-score
EBOX-ECAT-ZBPF 389 7 4.43 - 6.35
32Re-analysis of promoter organization
33Beyond the microarray
34Results of second database search
Framework of hits in human promoters four categories related to steroid metabolism z-score
EBOX-ECAT-ZBPF 961 16 4.36 - 6.25
35Statistics2 subtitle
Workflow
Literature analysis
Statistic analysis
Cellular processes
Sequence analysis
36Relaxed statistical approach
37Biology 2 subtitle
Workflow
Literature analysis
Statistic analysis
Cellular processes
Sequence analysis
38Merging profile and database searches
39Sterol biosynthesis and regulatory networks
ECAT EGRF ZBPF
40(No Transcript)
41Sterol biosynthesis and regulatory networks
ECAT EGRF ZBPF
GNF profile
42(No Transcript)
43Sterol biosynthesis / cell structure proteins and
regulatory networks
ECAT EGRF ZBPF
44PDGF conclusions
Conclusions
45(No Transcript)