Use case

QTL Microarray

Reference	Userreq.QtlMicroarray
High-level reqs	LargeData DatabaseStorage ComplexEvents Techreq.R BiomartQueries ErrorReporting ParamaterDescriptions ServiceAnnotation ArrayExpress
Proposed by	Paul Fisher

	Taverna 1.3	Taverna 2.0
Priority

Overview

building workflows to analyse qtls against microarray results (encompassing the recreation of the Grave's disease workflows)

Overall Goals

Be able to determine:

1. What genes in the QTL have changed (up-regulation/down-regulation)?

2. What pathways are the changed genes involved in?

3. What genes on the same pathway have changed – up-regulation in one place Vs down-regulation in another.

4. What pathways intersect with the QTL? Changed AND unchanged genes

Required services

Ensembl, Kegg, GO, Interproscan, Emboss

Maxd Arrayexpress, GEO

Workflow outline

Several workflows (or nested workflows) extract region of genome from ensembl that falls within the QTL

Analyse the QTL for genes

Determine which pathways these gene products are involved in

Extract affyids from QTL

Determine upregulation/downregulation

Compare Microarray results to QTL gene analysis

Appendix

Workflows already created for this use case can be found here: http://www.cs.man.ac.uk/~fisherp/