1. © 2004 by Genomatix Software GmbH Genomatix Dr. Martin Seifert Genomatix Software GmbH Landsberger Strasse 6, D-80339 München http://www.genomatix.de

2. © 2004 by Genomatix Software GmbH Genomatix What data/analysis tools does Genomatix offer? What does Genomatix mean by “understanding gene regulation” ? How to apply the data & tools to “understand gene regulation” ? Which data/analysis tools will support my work best?

3. © 2004 by Genomatix Software GmbH Genomatix Understanding Gene Regulation

4. © 2004 by Genomatix Software GmbH Genomatix Overview Introduction to gene expression Regulation of gene expression Gene regulation in a genomic view

5. © 2004 by Genomatix Software GmbH Genomatix Introduction to gene expression

6. © 2004 by Genomatix Software GmbH Genomatix the correct genes… …are expressed in the correct cell… …at correct levels. Introduction to gene expression …over correct time intervalls… Prerequisite for correct cell behaviour

7. © 2004 by Genomatix Software GmbH Genomatix the correct genes… …are expressed in the correct cell… …at correct levels. …over correct time intervalls… What if… “additional gene” “gene loss” “overexpression” “wrong time intervall” Introduction to gene expression

8. © 2004 by Genomatix Software GmbH Genomatix Summary Correct cell behavior requires expression of… correct set of genes in time at the correct level tough logistic task ! Introduction to gene expression

9. © 2004 by Genomatix Software GmbH Genomatix Overview Introduction to gene expression Regulation of gene expression Gene regulation in a genomic view

10. © 2004 by Genomatix Software GmbH Genomatix Coding exons First exon Schematic organization of a gene - GLOSSARY Promoter DNA Non-coding exon Regulation of gene expression

11. © 2004 by Genomatix Software GmbH Genomatix Chromatin activation Translation Gene expression steps Epigenetics Protein Processed protein G-ppp- Primary transcript G-ppp- Primary transcript Genomic sequence Transcription Mature mRNA Regulation of gene expression

12. © 2004 by Genomatix Software GmbH Genomatix Gene regulation – Transcription regulation Protein complex binding Regulatory network Regulation of gene expression

13. © 2004 by Genomatix Software GmbH Genomatix Example: Diabetes (MODY) Protein complex binding Regulatory network Regulation of gene expression Insulin

14. © 2004 by Genomatix Software GmbH Genomatix Key – lock principle TFIIB TFIIE TFIIH IN R TFIID TFIIF RNA polymerase II TFIIA TBP proximal promoter core promoter distal promoter/ enhancer TF binding sites „DNA-looping“ TATA TF binding sites Transcription factor binding sites Protein complex binding Regulation of gene expression

15. © 2004 by Genomatix Software GmbH Genomatix Dependencies in expression regulation Promoter of Gene A Gene Y Gene XGene ZGene T Regulation of gene expression Protein

16. © 2004 by Genomatix Software GmbH Genomatix One lock – different keys Same lock – different keys: Same gene - different biological context Regulation of gene expression

17. © 2004 by Genomatix Software GmbH Genomatix Promoter logic Which combination is functional ? 50 TFBs = One promoter – many transcription factor binding sites (TFBs) Need help ? Regulation of gene expression 1.125.899.906.842.624 combinations

18. © 2004 by Genomatix Software GmbH Genomatix Example: Analysis of the RANTES promoter Fessele, S., Maier, H., Zischek, C., Nelson, P.J., Werner, T. (2002) Regulatory context is a crucial part of gene function Trends in Genetics 18, 60-63 (MEDLINE 1181130) Regulation of gene expression

19. © 2004 by Genomatix Software GmbH Genomatix Summary Understanding gene regulation : understanding transcription regulation The promoter of a gene is the element to “unlock” gene expression The key to “unlock” gene expression is a protein complex Different keys can unlock the same promoter Promoter analysis: Find all keys (protein complexes) which can unlock. Protein complex requires expression of genes -> gene dependencies

20. © 2004 by Genomatix Software GmbH Genomatix Overview Introduction to gene expression Regulation of gene expression Gene regulation in a genomic view

21. © 2004 by Genomatix Software GmbH Genomatix One gene = one promoter ? Genes can have alternative transcripts with alternative promoters Gen A Gene regulation in a genomic view

22. © 2004 by Genomatix Software GmbH Genomatix Comparative genomic map of the Glucokinase GCK Promoterset 1Promoterset 2 Hepatic promoter Pancreatic promoter Tanisawa et al., Mol. Endocrinol. 6, 1070-1081, 1992. Data from ElDorado Gene regulation in a genomic view

23. © 2004 by Genomatix Software GmbH Genomatix TF- genes with one promoter. 51% Mammalian TFs genes are enriched in alternative promoters TF- genes with Alternative transcripts and alternative promoters. 49% All genesTranscription factors Genes with alternative transcripts and one promoter. 17% Genes with Alternative transcripts and alternative promoters. 28% Genes with one transcript. 55% Data from ElDorado Gene regulation in a genomic view

24. © 2004 by Genomatix Software GmbH Genomatix transcript resolving expression array Pathway oriented expression analysis on microarrays Knowledge of alternative promoters enables transcript-specific probe design conventional Expression array 3’-probe transcript-specific probes Gene regulation in a genomic view

25. © 2004 by Genomatix Software GmbH Genomatix Alternative mapping of probes to genes for Affymetrix chips Laurent Gautier*1, Morten Møller 2, Lennart Friis-Hansen 2 and Steen Knudsen 1 Results: In a large number of cases, 36%, the probes matching a reference sequence were consistent with the grouping of probes by the manufacturer of the chips. For the remaining cases there were discrepancies and we show how that can affect the analysis of data. Conclusions: While the probes on Affymetrix arrays remain the same for several years,the biological knowledge concerning the genomic sequences evolves rapidly. Using up-to-date knowledge can apparently change the outcome of an analysis. Methods: We investigated how probes found on recent commercial microarrays for human genes (Affymetrix HG-U133A) were matching a recent curated collection of human transcripts:the NCBI RefSeq database BMC Bioinformatics. 2004 Aug 14;5(1):111 Genome annotation

26. © 2004 by Genomatix Software GmbH Genomatix Summary A gene can have alternative promoters and alternative transcripts For gene regulation oriented microarray analysis genome annotation is important Alternative promoter usage can be tissue and context specific

27. © 2004 by Genomatix Software GmbH Genomatix Genomatix data and tools

28. © 2004 by Genomatix Software GmbH Genomatix Products

29. © 2004 by Genomatix Software GmbH Genomatix Overview

30. © 2004 by Genomatix Software GmbH Genomatix Overview

31. © 2004 by Genomatix Software GmbH Genomatix BiblioSphere Literature data mining strategy using more than 350.000 quality Checked gene names, synonyms & Genomatix proprietary semantic relation concepts 3-D interactive view of gene relationships Context sensitive disambiguation techniques to minimize the number of false positive matches. Search strategy allows not only to find direct gene-gene co-citations but also yet unknown gene relations via interlinks. BiblioSphere

32. © 2004 by Genomatix Software GmbH Genomatix BiblioSphere Classification of results with biological meaningful filters: Tissue, Gene Ontology and MeSH Statistical rating by z-scores for Gene Ontology, MeSH and tissue filters indicating over and under representation of co-cited genes in the referring biological categories Transcription factor analysis of the promoters of co-cited genes Literature analysis and evaluation by additional lines of evidences! Full interconnection with GEMSLauncher and ElDorado BiblioSphere

33. © 2004 by Genomatix Software GmbH Genomatix Overview

34. © 2004 by Genomatix Software GmbH Genomatix ElDorado genome annotation and analysis Most comprehensive genome annotation for regulatory regions and transcripts Integrated promoter annotation by promoter modules, pre-calculated by GEMS Launcher ElDorado Comparative genomics to detect and annotate unknown promoter regions (patent pending) Integrated SNP annotation according to effects for gene regulation and protein level Full interconnection with GEMSLauncher and BiblioSphere

35. © 2004 by Genomatix Software GmbH Genomatix Overview

36. © 2004 by Genomatix Software GmbH Genomatix GEMSLauncher Genomic sequences, mRNA, cDNA, SNPs SMARTest Exon Mapper Promoters PromterInspector Sequence Annotation S/MARExon/Intron structure Experimental results and literature TF Binding sites Modules, LTR, Genomic repeat MatDefine SMAR Librarys MatInspector SequenceShaperSNPInspectorModellInspector FastMFrameWorker Models Analysis Modelling

37. © 2004 by Genomatix Software GmbH Genomatix Genomic sequences, mRNA, cDNA, SNPs Bridging the gap between sequences, literature and experimental results Experimenteal results Genome annotation Literature mining Sequence analysis ElDorado BiblioSphereGEMS Launcher Understanding gene regulation Literature

38. © 2004 by Genomatix Software GmbH Genomatix Practical Example

39. © 2004 by Genomatix Software GmbH Genomatix Let’s have a break…