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Genomatix Dr. Martin Seifert Genomatix Software GmbH Landsberger Strasse 6, D-80339 München http://www.genomatix.de © 2004 by Genomatix Software GmbH Genomatix What does Genomatix mean by “understanding gene regulation” ? Which data/analysis tools will support my work best? What data/analysis tools does Genomatix offer? How to apply the data & tools to “understand gene regulation” ? © 2004 by Genomatix Software GmbH Genomatix Understanding Gene Regulation © 2004 by Genomatix Software GmbH Genomatix Overview Introduction to gene expression Regulation of gene expression Gene regulation in a genomic view © 2004 by Genomatix Software GmbH Genomatix Introduction to gene expression © 2004 by Genomatix Software GmbH Genomatix Introduction to gene expression Prerequisite for correct cell behaviour the correct genes… …are expressed in the correct cell… …over correct time intervalls… …at correct levels. © 2004 by Genomatix Software GmbH Genomatix Introduction to gene expression What if… the correct genes… “gene loss” “additional gene” …are expressed in the correct cell… “wrong time intervall” …over correct time intervalls… “overexpression” …at correct levels. © 2004 by Genomatix Software GmbH Genomatix Introduction to gene expression Summary Correct cell behavior requires expression of… correct set of genes in time at the correct level tough logistic task ! © 2004 by Genomatix Software GmbH Genomatix Overview Introduction to gene expression Regulation of gene expression Gene regulation in a genomic view © 2004 by Genomatix Software GmbH Genomatix Regulation of gene expression Schematic organization of a gene - GLOSSARY First exon DNA Promoter Coding exons Non-coding exon © 2004 by Genomatix Software GmbH Genomatix Regulation of gene expression Gene expression steps Translation Transcription Epigenetics Genomic sequence G-ppp- Primary transcript Mature mRNA Protein Chromatin activation Processed protein © 2004 by Genomatix Software GmbH Genomatix Regulation of gene expression Gene regulation – Transcription regulation binding Protein complex Regulatory network © 2004 by Genomatix Software GmbH Genomatix Regulation of gene expression Example: Diabetes (MODY) Insulin binding Protein complex Regulatory network © 2004 by Genomatix Software GmbH Genomatix Regulation of gene expression Key – lock principle Protein complex binding „DNA-looping“ distal promoter/ enhancer TF binding sites TF binding sites TBP TATA proximal promoter TFIIB TFIIE TFIIA TFIIF TFIID TFIIH core promoter IN R RNA polymerase II Transcription factor binding sites © 2004 by Genomatix Software GmbH Genomatix Regulation of gene expression Dependencies in expression regulation Promoter of Gene A Protein Gene X Gene Y Gene Z Gene T © 2004 by Genomatix Software GmbH Genomatix Regulation of gene expression One lock – different keys TBP TATA TFIIB TFIIE TFIIA TFIIFTFIID TFIIH TBP TATA TFIIB TFIIE TFIIA TFIIFTFIID TFIIH IN R Same lock – different keys: Same gene - different biological context © 2004 by Genomatix Software GmbH Genomatix Regulation of gene expression Promoter logic One promoter – many transcription factor binding sites (TFBs) Which combination is functional ? 50 TFBs = 1.125.899.906.842.624 combinations Need help ? © 2004 by Genomatix Software GmbH Genomatix Regulation of gene expression 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) © 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 Protein complex requires expression of genes -> gene dependencies Different keys can unlock the same promoter Promoter analysis: Find all keys (protein complexes) which can unlock. © 2004 by Genomatix Software GmbH Genomatix Overview Introduction to gene expression Regulation of gene expression Gene regulation in a genomic view © 2004 by Genomatix Software GmbH Genomatix Gene regulation in a genomic view One gene = one promoter ? Gen A Gen A Gen A Genes can have alternative transcripts with alternative promoters © 2004 by Genomatix Software GmbH Genomatix Gene regulation in a genomic view Comparative genomic map of the Glucokinase GCK Promoterset 1 Pancreatic promoter Promoterset 2 Hepatic promoter Data from ElDorado Tanisawa et al., Mol. Endocrinol. 6, 1070-1081, 1992. © 2004 by Genomatix Software GmbH Genomatix Gene regulation in a genomic view Mammalian TFs genes are enriched in alternative promoters All genes Genes with alternative transcripts and one promoter. 17% Genes with Alternative transcripts and alternative promoters. 28% Transcription factors TF- genes with one promoter. 51% Genes with one transcript. 55% TF- genes with Alternative transcripts and alternative promoters. 49% Data from ElDorado © 2004 by Genomatix Software GmbH Genomatix Gene regulation in a genomic view Pathway oriented expression analysis on microarrays transcript-specific probes transcript resolving expression array 3’-probe conventional Expression array Knowledge of alternative promoters enables transcript-specific probe design © 2004 by Genomatix Software GmbH Genomatix Genome annotation Alternative mapping of probes to genes for Affymetrix chips Laurent Gautier*1 , Morten Møller 2 , Lennart Friis-Hansen 2 and Steen Knudsen 1 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 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. BMC Bioinformatics. 2004 Aug 14;5(1):111 © 2004 by Genomatix Software GmbH Genomatix Summary A gene can have alternative promoters and alternative transcripts Alternative promoter usage can be tissue and context specific For gene regulation oriented microarray analysis genome annotation is important © 2004 by Genomatix Software GmbH Genomatix Genomatix data and tools © 2004 by Genomatix Software GmbH Genomatix Products © 2004 by Genomatix Software GmbH Genomatix Overview © 2004 by Genomatix Software GmbH Genomatix Overview © 2004 by Genomatix Software GmbH Genomatix BiblioSphere 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. © 2004 by Genomatix Software GmbH Genomatix BiblioSphere 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 Full interconnection with GEMSLauncher and ElDorado Literature analysis and evaluation by additional lines of evidences! © 2004 by Genomatix Software GmbH Genomatix Overview © 2004 by Genomatix Software GmbH Genomatix ElDorado ElDorado genome annotation and analysis Most comprehensive genome annotation for regulatory regions and transcripts Comparative genomics to detect and annotate unknown promoter regions (patent pending) Integrated promoter annotation by promoter modules, pre-calculated by GEMS Launcher Integrated SNP annotation according to effects for gene regulation and protein level Full interconnection with GEMSLauncher and BiblioSphere © 2004 by Genomatix Software GmbH Genomatix Overview © 2004 by Genomatix Software GmbH Genomatix GEMSLauncher Genomic sequences, mRNA, cDNA, SNPs SMARTest Sequence Annotation Analysis PromterInspector S/MAR Promoters SNPInspector SequenceShaper Modelling MatInspector SMAR Exon Mapper Exon/Intron structure ModellInspector Models FrameWorker FastM TF Binding sites Librarys MatDefine Modules, LTR, Genomic repeat Experimental results and literature © 2004 by Genomatix Software GmbH Genomatix Genomatix Bridging the gap between sequences, literature and experimental results Genomic sequences, mRNA, cDNA, SNPs ElDorado Genome annotation Understanding gene regulation BiblioSphere Literature mining Experimenteal results GEMS Launcher Sequence analysis Literature © 2004 by Genomatix Software GmbH Genomatix Practical Example © 2004 by Genomatix Software GmbH Genomatix Let’s have a break… © 2004 by Genomatix Software GmbH