Annotation and Analysis of Microarray Data .ppt

Annotation and Analysis of Microarray DataA primer for NERC researchers Data and the NERC Data is an asset Data may have unforeseen uses Analysis loses information Bulk analysis and data mining needs “uniform” data Data stored without adequate annotation is useless Data rescue is expensive and unreliable Metadata and Microarrays Sequence data is static Post-genome is very state-dependant Transcriptome = no. of cell types * no. of environmental conditions Annotation matters Data comparisons matter We need to take lessons from the gene debacle Protein-tyrosine phosphatase, non-receptor type 6, Protein-tyrosine phosphatase 1C, PTP-1C, Hematopoietic cell protein-tyrosine phosphatase, SH-PTP1, Protein-tyrosine phosphatase SHP-1 LARD, death receptor 3 beta, WSL-1R protein, lymphocyte associated receptor of death, death receptor 3 Metadata standards and data repositories What is MIAME? MIAME is the internationally adopted standard for the Minimal Information About a Microarray Experiment. The result of a MGED () driven effort to codify the description of a microarray experiment. MIAME aims to define the core that is common to most experiments. Ultimately, it tries to specify the collection of information that would be needed to allow somebody to completely reproduce an experiment that was performed elsewhere. The Six Parts of MIAME Experimental design: the set of hybridization experiments as a whole Array design: each array used and each element (spot, feature) on the array Samples: samples used, extract preparation and labeling Hybridizations: procedures and parameters Measurements: images, quantification and specifications Normalization controls: types, values and specifications MIAME definitions Available from All details mentioned in MIAME should be captured Latest draft: Version 1.1 (Draft 5, March 5, 2002) See also: A. Brazma, et al., Nature Genetics, vol 29 (December 2001), pp 365 - 371 But… Environmental genomics is a diverse, heterogeneous discipline,