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Microarray Evaluation for

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Title: Microarray Evaluation for


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