Microarraydna
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This document discusses DNA microarray analysis and its use in studying Down syndrome. Microarrays allow measurement of expression levels of thousands of genes simultaneously. The analysis process includes importing data, checking for abnormalities, normalizing expression levels, differential analysis between conditions, and filtering results. A case study on Down syndrome is presented, where microarray analysis found increased expression of genes on chromosome 21, including COL6A1, SOD1, CBS, and DYRK1A, consistent with the extra copy of chromosome 21 causing overexpression of genes involved in trisomy 21.
1 of 40
Downloaded 14 times
![Output data?
> exprs(mydata)[1:10,]
Down Syndrome-Astrocyte-1478-1-U133A.CEL
1 142.0
2 9543.8
3 163.0
4 9706.8
5 48.3
6 133.5
7 8966.0
8 129.0](https://image.slidesharecdn.com/microarraydna-130628110833-phpapp01/85/Microarraydna-13-320.jpg)
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Microarraydna
- 2. DNA Microarray Analysis DNA Microarray Analysis
- 3. DNA
- 6. DNA?
- 7. Genes
- 9. Microarrays
- 13. Output data? > exprs(mydata)[1:10,] Down Syndrome-Astrocyte-1478-1-U133A.CEL 1 142.0 2 9543.8 3 163.0 4 9706.8 5 48.3 6 133.5 7 8966.0 8 129.0
- 14. Output data? > mydata AffyBatch object size of arrays=712x712 features (29 kb) cdf=HG-U133A (22283 affyids) number of samples=25 number of genes=22283 annotation=hgu133a notes=
- 15. RoadMap
- 16. Analysis
- 17. Case Study
- 18. Down Syndrome
- 19. Trisomy
- 20. In trisomy 21, the presence of an extra set of genes leads to overexpression of the involved genes, leading to increased production of certain products.
- 21. Suspects COL6A1ETS2 Superoxide Dismutase (SOD1) CAF1A Cystathione Beta Synthase (CBS) DYRK CRYA1 GART IFNAR
- 22. RrrrrRRRrrr
- 23. R
- 24. How to deal with the data? Import Check for abnormalities Normalize Differential analysis Filtering Output
- 25. Import
- 26. DataSet
- 27. Global up-regulation of chromosome 21 gene expression in the developing Down syndrome brain Mao et al., Genomics
- 29. Check
- 31. Normalize
- 32. Before
- 33. After
- 37. The results
- 38. Ensembl Gene ID HGNC symbol Chromosome Name 1 ENSG00000060491 OGFR 20 2 ENSG00000073536 NLE1 17 3 ENSG00000115596 WNT6 2 4 ENSG00000116176 TPSG1 16 5 ENSG00000118217 ATF6 1 6 ENSG00000130640 TUBGCP2 10 7 ENSG00000131096 PYY 17 8 ENSG00000132507 EIF5A 17 9 ENSG00000135823 STX6 1 10 ENSG00000137504 CREBZF 11 11 ENSG00000141959 PFKL 21 12 ENSG00000142168 SOD1 21 13 ENSG00000143184 XCL1 1 14 ENSG00000154719 MRPL39 21 15 ENSG00000154723 ATP5J 21 16 ENSG00000155313 USP25 21 17 ENSG00000156256 USP16 21 18 ENSG00000157538 DSCR3 21 19 ENSG00000159140 SON 21 20 ENSG00000159147 DONSON 21 21 ENSG00000159788 RGS12 4 22 ENSG00000159961 OR3A3 17 23 ENSG00000160209 PDXK 21 24 ENSG00000160213 CSTB 21 25 ENSG00000160221 C21orf33 21 26 ENSG00000160294 MCM3AP 21 27 ENSG00000167515 TRAPPC2L 16
- 40. Thanks !