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

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

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

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.

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

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

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

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

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

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

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.

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...

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.

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

Maxd Microarray Group, University of Manchester http://www.bioinf.man.ac.uk/microarray/maxd 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

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

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

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

MaxdMaker Screen shot of maxdmaker

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

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

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)

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

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