WORKSHOP - WORKING WITH ARABIDOPSIS AFFYMETRIX DATA
Fridays, the 25-feb and 4-march 2005
A14 (Plant Sciences Computer Room)

BACKGROUND:

The workshop will concentrate on availability, normalisation and a variety of further analysis tools for Affymetrix data, both your own and that which is publicly available. It will be open to anyone in any of the TARGET and/or plant science groups.

It will not concentrate on the practical side of Affymetrix chips which has been previously covered in John Okyere's TARGET talk, which may be of interest.

The following talks (from the Graduate School Course on Post-genomics and bio-informatics) from may be useful:
Introduction to transcriptomics, microarrays versus gene chips (Neil Graham)
Analysing transcriptome data (John Hammond [Warwick HRI])
J-Express tutorial guide (Paddy Tighe) (uses spotted array data, not affy data)
Experimental design and statistics (John Okyere)
Analysing transcriptome data - a practical example (Martin Broadley)
Standards and data storage issues arising from transcriptome experiments (David Craigon)

Also of interest, may be Daniel Zadik's Arabidopsis Affymetrix Data-Mining Tool Links page.

SCHEDULE:

25 Feb – Data Sources, Normalisation and NASC Affy Site

2pm - Introduction (Sean May, NASC)

210 - Normalisation and Analysis of the Affymetrix data (David Craigon, NASC)
- Basic Principals of Normalisation and Analysis
- MAS4, MAS5 and GCOS
- Perfect-Match Versus Perfect-Match-and-MisMatch
- Alternatives to MAS5 (J-Express, GeneSpring, D-Chip, RMA, …)

250 - Experiences with J-Express (Zoë Wilson)

310 - Genespring (Martin Broadley)

320 - Data Availability and NASC tools (Beatrice Schildknecht, NASC)
- NASCAffy website
- NASCAffy data
- NASC tools (spot history, gene swinger, two gene scatterplot, bulk gene download)

340 - Practical Session
- Let me know whether you found the practical useful

530 - finish

4 March – Tools for Further Analysis

2pm - Introduction (Daniel Zadik)

210 - DNA-Chip analyzer dChip (Gema Vizcay-Barrena)
- dChip website
- Normalisation tool, in addition to those talked about last week.

225 - Expression Profile Clustering (Daniel Zadik)
- EPClust website
- Clustering and Promoters
- PLANTcare website

240 - Using Expression data to suggest Pathways (Paddy Tighe)
- Pathway-Assist
- J-Express
- Gene Ontology

300 - Tea Break, by popular demand!

315 - GenevestigATor "Toolbox" (Daniel Zadik)
- GenevestigATor website
- Digital Northern
- Gene Atlas
- Response Viewer
- Meta-Analyser
- Gene Correlator
- Gene Chronologer
- Mutant Surveyor

330 - An Excel Macro to Visualise Patterns for Chosen Genes (Daniel Zadik)

340 - Selection of Candidate Genes from Affymetrix Data
- E.g.1: genes involved with fibre formation (Susana Ubeda-Tomas)
- E.g.2: germination, mutants and developmental signatures (Mike Holdsworth)
- E.g.3: genes involved with pollen and flower development (Gema Vizcay-Barrena)

430 - Finish or Practical Session
- Try out the software you have heard about or
- Let me know whether you think the organised practical sessions are useful

530 - Latest Possible Finish

QUESTIONS:

Do you want future, more focused workshops on any of the above sections? (reply)

Also do people want to learn about other types of microarray (e.g. cDNA) in future workshops? (reply)

Plant Science Division

Further information on Arabidopsis