DNA Microarray Analysis

Daniel Kosalla

DNA Microarray Analysis

• DNA

• Microarray

• Analysis

DNA

DNA?

Genes

Gene expression

Microarrays

What are microarrays?

Output data?> exprs(mydata)[1:10,] Down Syndrome-Astrocyte-1478-1-U133A.CEL1 142.02 9543.83 163.04 9706.85 48.36 133.57 8966.08 129.0

Output data?

> mydataAffyBatch objectsize of arrays=712x712 features (29 kb)cdf=HG-U133A (22283 affyids)number of samples=25number of genes=22283annotation=hgu133anotes=

RoadMap

Analysis

Case Study

Down Syndrome

Trisomy

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.

Suspects

• COL6A1ETS2• Superoxide Dismutase (SOD1)• CAF1A• Cystathione Beta Synthase (CBS)• DYRK• CRYA1• GART• IFNAR

RrrrrRRRrrr

R

How to deal with the data?

• Import

• Check for abnormalities

• Normalize

• Differential analysis

• Filtering

• Output

Import

DataSet

“Global up-regulation of chromosome 21 gene expression

in the developing Down syndrome brain”Mao et al., Genomics

Check

Normalize

Before

After

Differential analysis

The results

Ensembl Gene ID HGNC symbol Chromosome Name1 ENSG00000060491 OGFR 202 ENSG00000073536 NLE1 173 ENSG00000115596 WNT6 24 ENSG00000116176 TPSG1 165 ENSG00000118217 ATF6 16 ENSG00000130640 TUBGCP2 107 ENSG00000131096 PYY 178 ENSG00000132507 EIF5A 179 ENSG00000135823 STX6 110 ENSG00000137504 CREBZF 1111 ENSG00000141959 PFKL 2112 ENSG00000142168 SOD1 2113 ENSG00000143184 XCL1 114 ENSG00000154719 MRPL39 2115 ENSG00000154723 ATP5J 2116 ENSG00000155313 USP25 2117 ENSG00000156256 USP16 2118 ENSG00000157538 DSCR3 2119 ENSG00000159140 SON 2120 ENSG00000159147 DONSON 2121 ENSG00000159788 RGS12 422 ENSG00000159961 OR3A3 1723 ENSG00000160209 PDXK 2124 ENSG00000160213 CSTB 2125 ENSG00000160221 C21orf33 2126 ENSG00000160294 MCM3AP 2127 ENSG00000167515 TRAPPC2L 16

Thanks !