© 2004 by Genomatix Software GmbH Genomatix Dr. Martin Seifert Genomatix Software GmbH Landsberger...

© 2004 by Genomatix Software GmbH

Genomatix

Dr. Martin Seifert

Genomatix Software GmbH

Landsberger Strasse 6, D-80339 München

http://www.genomatix.de


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?


Genomatix

Understanding Gene Regulation


Genomatix

Overview

Introduction to gene expression

Regulation of gene expression

Gene regulation in a genomic view


Genomatix Introduction to gene expression


Genomatix

the correct genes…

…are expressed inthe correct cell…

…at correct levels.


…over correct time intervalls…

Prerequisite for correct cell behaviour


Genomatix

the correct genes…

…are expressed inthe correct cell…

…at correct levels.…over correct time intervalls…

What if…

“additional gene”

“gene loss”

“overexpression”“wrong time intervall”



Genomatix

Summary

Correct cell behavior requires expression of…

correct set of genes

in time

at the correct level

tough logistic task !



Genomatix

Overview





Genomatix

Coding exons

First exon

Schematic organization of a gene - GLOSSARY

Promoter

DNA

Non-coding exon



Genomatix

Chromatin activation

Translation

Gene expression steps

Epigenetics

Protein

Processed protein

G-ppp-

Primary transcript

G-ppp-

Primary transcript

Genomic sequence

Transcription

Mature mRNA



Genomatix

Gene regulation – Transcription regulation

Protein complex

binding

Regulatory network



Genomatix

Example: Diabetes (MODY)

Protein complex

binding

Regulatory network


Insulin


Genomatix

Key – lock principle

TFIIB TFIIE

TFIIH

INR

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



Genomatix

Dependencies in expression regulation

Promoter of Gene A

Gene YGene X Gene Z Gene T


Protein


Genomatix

One lock – different keys

TFIIB TFIIE

TFIIH TFIID TFIIF TFIIA

TBP TATA

TFIIB TFIIE

TFIIH

INR

TFIID TFIIF TFIIA

TBP TATA

Same lock – different keys: Same gene - different biological context



Genomatix

Promoter logic

Which combination is functional ?

50 TFBs =

One promoter – many transcription factor binding sites (TFBs)

Need help ?


1.125.899.906.842.624 combinations


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 functionTrends in Genetics 18, 60-63 (MEDLINE 1181130)



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


Genomatix

Overview





Genomatix

One gene = one promoter ?

Genes can have alternative transcripts with alternative promoters

Gen A

Gen A

Gen A



Genomatix

Comparative genomic map of the Glucokinase GCK

Promoterset 1 Promoterset 2

Hepatic promoter

Pancreatic promoter

Tanisawa et al., Mol. Endocrinol. 6, 1070-1081, 1992.

Data from ElDorado



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 genes Transcription 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



Genomatix

transcript resolvingexpression array

Pathway oriented expression analysis on microarrays

Knowledge of alternative promoters enables transcript-specific probe design

conventional Expression array

3’-probetranscript-specific probes



Genomatix

Alternative mapping of probes to genes for Affymetrix chipsLaurent 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


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


Genomatix

Genomatix data and tools


Genomatix

Products


Genomatix

Overview


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


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


Genomatix

Overview


Genomatix

ElDorado genome annotation and analysis

Most comprehensive genome annotation for regulatory regions andtranscripts

Integrated promoter annotation by promoter modules, pre-calculated byGEMS Launcher

ElDorado

Comparative genomics to detect and annotate unknown promoter regions (patent pending)

Integrated SNP annotation according to effects for gene regulationand protein level

Full interconnection with GEMSLauncher and BiblioSphere


Genomatix

Overview


Genomatix GEMSLauncher

Genomic sequences, mRNA, cDNA, SNPs

SMARTest Exon Mapper

Promoters

PromterInspectorSequenceAnnotation

S/MAR Exon/Intron structure

Experimental results and literature

TF Binding sites Modules, LTR,

Genomic repeatMatDefine

SMAR

Librarys

MatInspector

SequenceShaperSNPInspector ModellInspector

FastMFrameWorker

ModelsAnalysis

Modelling


Genomatix Genomatix

Genomic sequences, mRNA, cDNA, SNPs

Bridging the gap between sequences, literature and experimental results

Experimenteal results

Genome annotation

Literature mining Sequence analysis

ElDorado

BiblioSphere GEMS Launcher

Understandinggene regulation

Literature


Genomatix

Practical Example


Genomatix

Let’s have a break…

© 2004 by Genomatix Software GmbH Genomatix Dr. Martin Seifert Genomatix Software GmbH Landsberger...

Documents

Transcript of © 2004 by Genomatix Software GmbH Genomatix Dr. Martin Seifert Genomatix Software GmbH Landsberger...