Beyond The Gene List: Using Bioinformatics To Make Sense Out Of Array Data

1) Introduction 2) What is a microarray? a) Experimental steps in a typical cDNA microarray experiment b) If you don?t see it, it doesn?t mean that it isn?t there. 3) Experimental Design a) Comparing independent ?replicate? arrays b) ?A vs. M? plot. 4) Informatic Annotation of Array Data 5) Initial annotation of gene list based on published literature a) Linking array data to the literature b) GenMAPP c) PubGene 6) Databases— The need for public databases for gene expression annotation and analysis. 7) Data Mining And Annotation By Chromosome a) Data reduction. b) Assessing chromosomal location using genome databases. c) Using databases of other array experiments to annotate gene functions. d) Validate informatic hypotheses prospectively 8) Using Microarrays to study underlying regulatory mechanisms a) Identify co-regulated genes. b) Collect 5kb upstream of transcription start site. c) Perform similarity search to identify shared sequences. d) Promotor/Enhancer Motif Search e) Follow-up shared sequences to identify putative TF binding sites. f) Pitfalls/Suggestions 9) Summary and Acknowlegements 10) Resources Nervous system development and function in part depends on the careful orchestration of gene expression in the CNS. The magnitude of the problem of understanding this system from a molecular standpoint is underscored by the estimate that more than half of all genes are expressed in the nervous system and many of them are relatively specific to the brain. Currently, there are many different high throughput methods to examine gene expression in different cells, tissues or even pathological specimens under various conditions, including serial analysis of gene expression (SAGE)(Velculescu, Zhang et al. 1995) large-scale cDNA sequencing (Okubo, Hori et al. 1992), and DNA microarrays (Schena, Shalon et al. 1995). All of these approaches rely heavily on use of informatics for interpretation. In addition, there are now pure informatic approaches available now, which include expressed sequence tag (EST) database comparison (O'Dowd, Nguyen et al. 1998), and mining of SAGE or other databases. This syllabus focuses on DNA microarrays. Oligonucleotide and cDNA arrays enable the monitoring of thousands of known and unknown genes in parallel in many samples in an efficient Due to the high throughput nature of this approach, large amounts of data are generated in a single experiment. Formerly, cost and availability of microarrays were limitations to performing experiments, but as these issues are resolved, the new limitation becomes interpretation and analysis. The ability to study gene expression on a genomic level using microarrays raises …