1. Gene Expression BMI 731 Winter 2005 Catalin Barbacioru Department of Biomedical Informatics Ohio State University

2. Thesis: the analysis of gene expression data is going to be big in 21st century statistics Many different technologies, including Spotted DNA arrays (Brown/Botstein) Short oligonucleotide arrays (Affymetrix) Serial analysis of gene expression (SAGE) Long oligo arrays (Agilent) Fibre optic arrays (Illumina)

3. 1995 1996 1997 1998 1999 2000 2001 0 100 200 300 400 500 600 (projected) Year Number of papers Total microarray articles indexed in Medline

4. Common themes Parallel approach to collection of very large amounts of data (by biological standards) Sophisticated instrumentation, requires some understanding Systematic features of the data are at least as important as the random ones Often more like industrial process than single investigator lab research Integration of many data types: clinical, genetic, molecular…..databases

5. Central dogma The expression of the genetic information stored in the DNA molecule occurs in two stages: (i) transcription, during which DNA is transcribed into mRNA; (ii) translation, during which mRNA is translated to produce a protein. DNA → mRNA → protein Other important aspects of gene regulation: methylation, alternative splicing.

6. Idea: measure the amount of mRNA to see which genes are being expressed in (used by) the cell. Measuring protein might be better, but is currently harder.

17. DNA microarrays represent an important new method for determining the complete expression profile of a cell. Monitoring gene expression lies at the heart of a wide variety of medical and biological research projects, including classifying diseases, understanding basic biological processes, and identifying new drug targets.

18. Affymetrix ® Instrument System Platform for GeneChip ® Probe Arrays Integrated Integrated Easy to use Easy to use Exportable Exportable Versatile Versatile

19. Photolithography

20. Synthesis of Ordered Oligonucleotide Arrays O O O O OO O O O O Light (deprotection) HO HO O O O T T O O OT T O O O T T C C OT T C C O Light (deprotection) T T O O OT T O O O C A T A TC A T A T A G C T GA G C T G T T C C GT T C C G Mask Substrate Mask Substrate T – C – REPEAT

21. Affymetrix GeneChip arrays

22. GeneChip ® Probe Arrays 24µm Millions of copies of a specific oligonucleotide probe Image of Hybridized Probe Array Image of Hybridized Probe Array >200,000 different complementary probes Single stranded, labeled RNA target Oligonucleotide probe * * * * *1.28cm GeneChip Probe Array Hybridized Probe Cell

25. Perfect Match (PM) Mis Match (MM) Control log(PM / MM) = difference score All significant difference scores are averaged to create “average difference” = expression level of the gene. Each pixel is quantitated and integrated for each oligo feature (range 0-25,000) Analysis of expression level from probe sets

26. each oligo sequence (20-25 mer) is synthesized as a 20 µ square (feature) each feature contains > 1 million copies of the oligo scanner resolution is about 2 µ (pixel) each gene is quantitated by 16-20 oligos and compared to equal # of mismatched controls 22,000 genes are evaluated with 20 matching oligos and 10 mismatched oligos = 480,000 features/chip 480,000 features are photolithographically synthesized onto a 2 x 2 cm glass substrate Analysis of expression level from probe sets

27. Affymetrix arrays Global views of gene expression are often essential for obtaining comprehensive pictures of cell function. For example, it is estimated that between 0.2 to 10% of the 10,000 to 20,000 mRNA species in a typical mammalian cell are differentially expressed between cancer and normal tissues. Whole-genome analyses also benefit studies where the end goal is to focus on small numbers of genes, by providing an efficient tool to sort through the activities of thousands of genes, and to recognize the key players. In addition, monitoring multiple genes in parallel allows the identification of robust classifiers, called "signatures", of disease. Global analyses frequently provide insights into multiple facets of a project. A study designed to identify new disease classes, for example, may also reveal clues about the basic biology of disorders, and may suggest novel drug targets.

30. Spotted DNA microarrays In ‘‘spotted’’ microarrays, slides carrying spots of target DNA are hybridized to fluorescently labeled cDNA from experimental and control cells and the arrays are imaged at two or more wavelengths Expression profiling involves the hybridization of fluorescently labeled cDNA, prepared from cellular mRNA, to microarrays carrying thousands of unique sequences. Typically, a set of target DNA samples representing different genes is prepared by PCR and transferred to a coated slide to form a 2-D array of spots with a center-to-center distance (pitch) of about 200 μm, providing a pan-genomic profile in an area of 3 cm2 or less. cDNA samples from experimental and control cells are labeled with different color fluors (cytochrome Cy5 and Cy3) and hybridized simultaneously to microarrays, and the relative levels of mRNA for each gene are then determined by comparing red and green signal intensities

31. Spotted DNA microarrays Scanning Technology Microarray slides are imaged with a modified fluorescence microscope designed for scanning large areas at high resolution (arrayWoRx, Applied Precision, Issaquah, WA, Affymetrix). Fluorescence illumination are obtained from a metal halide arc lamp focused onto a fiber optic bundle, the output of which is directed at the microarray slide and emission recorded through a microscope objective (Nikon) onto a cooled CCD (charge-coupled device) camera. Interference filters are used to select the excitation and emission wavelengths corresponding to the Cy3 and Cy5 fluorescent probes (Amersham Pharmacia). Each image covered a 2.4 x 2.4 mm area of the slide at 5-μm resolution. To scan the entire microarray, a series of images (‘‘panels’’) were acquired by moving the slide under the microscope objective in 2.4-mm increments.

32. http://www.bio.davidson.edu/course s/genomics/chip/chip.swf

38. The red/green ratios can be spatially biased. Top 2.5%of ratios red, bottom 2.5% of ratios green

40. Spotted vs. Affymetrix Arrays Affymetrix strengths: - highly reliable: synthesized in situ - highly reproducible from run to run - no clone maintenance or ‘drift’ - sealed fluidics and controlled temperature - standardized chips increase database power - excellent scanner - complex, but very reliable labelling - excellent cost/benefit ratio - amenable to mutation and SNP detection

41. Affymetrix weaknesses/limitations - not easily customized: $300K/chip - high labeling cost $170/chip - high per chip cost $350 to $1850 - limited choice of species - requires knowledge of sequence - not designed for competitive protocols

42. Limitations to all microarrays - dynamic range of gene expression: very difficult to simultaneously detect low and high abundance genes accurately - each gene has multiple splice variants 2 splice variants may have opposite effects (i.e. trk) arrays can be designed for splicing, but complexity ^ 5X - translational efficiency is a regulated process: mRNA level does not correlate with protein level - proteins are modified post-translationally glycosylation, phosphorylation, etc. - pathogens might have little ‘genomic’ effect

45. Biological question Differentially expressed genes Sample class prediction etc. Testing Biological verification and interpretation Microarray experiment Estimation Experimental design Image analysis Normalization Clustering Discrimination R, G 16-bit TIFF files (Rfg, Rbg), (Gfg, Gbg)