1. Transcriptomics on Bio-Linux
Joe Wood
Introduction to transcriptomics software on Bio-Linux

2. Transcriptomics on Bio-Linux
GeneSpring and GeNet
Maxd
MIAME
EST pipeline
Talk will give an introduction to transcriptomics software on Bio-Linux.
1. Commercial microarray data analysis software GeneSpring from Silicon Genetics and its database back-end GeNet
2. Complementary to GeneSpring, the open-source microarray data analysis software MAXD – University of Manchester
3. Talk a bit about MIAME compliance within these software packages
4. EST pipeline in development for Bio-Linux

3. GeneSpring Silicon Genetics Installed on Bio-Linux
Licences available for EG grant holders
GeNet Database
MIAME compliant
From silicon genetics
pre-installed on biolinux
licences available EG grant holders
GeNet: silicon genetics
- data repository for genespring data
- installed in EGTDC
MIAME compliant
- minimum information about a microarry exp.
- standard which allows exchange of data and allow other people to analyse/interrogate your data and you theirs
Will talk about GeNet and MIAME a bit later

4. GeneSpring Features Data normalisation Data clustering
3D visualisation
Pathway views
Expression profile comparison
Scripting
Advanced statistical tools
Large range of features
Will go through each with screen shots, talk about GeNet and MIAME implemenation and give a brief demo
We run GeneSpring training courses – this is just an overview of what is there.

5. Data Normalisation 16 different normalisations available for data sets
user can define and save normalisation scenarios

6. Data clustering
Sophisticated clustering methods to find patterns in data
eg. hierarchical clustering
principal components analysis
-picks out significant data patterns

7. 3D Visualisation Interactive representations of complex data
user defined axes
can rotate figure with mouse

8. Expression Profile Comparison
Allows user to compare a particular expression pattern against experiments stored in GENET to pull out genes with similar expression patterns

9. Pathway Views
Genes + expression levels can be visualised in their pathways
user can define pathways or pull in publically available pathways

10. Advanced Statistical Tools
Range of statistical tools
eg. T-tests, analysis of varience
Work out truly differentially expressed genes

11. Scripting
With all the many options of analysis, normalisation and so on useful to save analysis
scripting allows this , making high-throughput analysis easier.
ScriptEditor for creating and editing these scripts comes bundled with version 5.1 of GeneSpring.

12. GeNet Data Repository Central database hosted by EGTDC
Store and share microarray data
GeNet Public Data Repository
~6500 MIAME annotated microarray experiments
Upload to GeneSpring as example data sets
GeNet – database solution from Silicon Genetics for storing microarray data in a central repository.
We hope to store data from EG program which can be submitted by labs remotely using genespring.
Silicon Genetics have recently released the GeNet Public Data Repository
Collection of 6500 microarray experiments from a variety of organisms drawn from public sources but also from some SG's contacts in industry.
People with logins to EGTDC GeNet can connect via GeneSpring and upload these data sets and try out normalisations etc.
These experiments are MIAME annotated. Go onto so explain a bit about MIAME in GeneSpring...

13. MIAME MIAME – minimum information about a microarray experiment
Standard for recording microarray experiments
Required by major journals inc. Nature and Lancet
MIAME/Env
MIAME – minimum information about at a microarray experiment
Standard for recording microarray data which to allow consistant and easy sharing and exchange of data
Recently major journals such as Nature,Cell and the Lancet require that all microarray data submitted for publication is MIAME compliant.
EGTDC is aiming to make MIAME the de facto standard within the Environmental genomics community.
Development of MIAME based on model organisms in a medical context. Toxigenomics community have extended MIAME to MIAME/Tox similarly EGTDC has formed a working group to develop MIAME/Env which will extend MIAME for the environmental genomics community.

14. MIAME and GeneSpring Controlled by standardattributes.xml
Defines which attributes for a particular sample must be entered
Required, recommended, optional
Set MIAME options to required – MIAME compliance
MIAME compliance controlled by a standardattributes.xml file
-download from the silicon genetics website
Users – this file defines and controls which attributes you need provide for a particular sample
attributes- required, recommended or optional
Miame attributes can be set to required in the file hence enforcing MIAME compliance

15. Maxd Microarray Group, University of Manchester
Open Source
Installed on Bio-Linux
Maxd is microarray analyis software package developed by
Andy Brass group in Manchester – EGTDC partners (very active in development of MIAME/Env)
Point out URL
Open Source ie. Free
and comes preinstalled on Bio-Linux

16. Maxd at EGTDC URL: http://envgen.nox.ac.uk/maxd.html Maxd homepage
Maxd course notes
Extra installation instructions
Maxd website EGTDC
Link to manchester site
Course notes from maxd course , manchester last sept.
Specific installation instructions written by oxford team

17. Maxd components MaxdMaker MaxdLoad MaxdView
Three different tools that make up maxd
Java applications:
maxdmaker – creates the maxd database
madload -loading data into schema in MIAME compliant manner
maxdview viewing and analysing data – equivalent of GeneSpring

18. MaxdMaker Maxd dataschema EBI -Array Express (MIAME) maxd.sql MySQL
PostgreSQL
Oracle
Creates the maxd datashema
Based on the Array Express schema developed at the EBI
MIAME (Minimal information about a microarray experiment) complient
Produces file maxd.sql
Series of commands in SQL(structured query language) which set up the database tables in DBMS
MySQL free
PostgreSQL free, more functionality
Oracle commercial
(Bio-Linux has MySQL and PostgreSQL pre-installed)
Resulting in a maxd database

19. MaxdMaker
Screen shot of maxdmaker

20. MaxdLoad Array scanner text file Maxd database
MaxdLoad is the piece of software used to load your raw data and associated (MIAME compliant!) data into the maxd database you have just created
Screenshot of the database browser in maxdLoad

21. MaxdView Array scanner text file Maxd database
MaxdView -analysis software for viewing and analysing microarray data
Can be used with raw data or data uploaded from maxd database.
(Equivalent to GeneSpring using raw data or GeNet Data)
A wide variety of views shown in this screenshot
Clusters, scatter plot, graph plots and a host of ways of manipulating normalisations and clusters
For programmers – ability to write plugins for you own analyses

22. Why maxd? Open source MIAME compliant Complement to GeneSpring
Extra analysis methods
Open source -– free and possible to modify the source code
MIAME – linked to the MIAME effort submit data to and bring in data from conforming public databases
Complements GeneSpring on Bio-Linux as it has some extra analysis methods (eg. Benfords Law)

23. EST Pipeline Bio-Linux EST pipeline in development Trace files
EST sequences
Clustered
Annotated
Submit to dbEST
An EST pipeline is in development for Bio-Linux

24. Integrating GeneSpring/EST
GeneSpring 'genomes'
GeneSpider automatically annotates
GeneTable files
Can create own GeneTables
EST annotations, other lab-specific annotations
Genespring has 'genomes'
effecitively all the sequences on the chip your are analysing
These can be automatically annotated with GeneSpider within genespring which searches the web and annotates your sequence.
Stored in GeneTable files
If you have your own annotations for example generated from EST pipeline you can make own GeneTable files and use the annotations within GeneSpring