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Transcript 
A cell and its population of genes:
DNA forms double strands by a process called
hybridization:
Labeling
Hybridization
m109 oligo
placenta complex
2 color fluoresent dye labeled mRNA
Affymetrix oligonucleotide arrays
Illumina bead arrays
• Illumina flyer
SNP detection
(slide from NCBI,
http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/TechBeadArray.shtml
RNA-seq
From:
RNA-Seq: a revolutionary
tool for transcriptomics
Zhong Wang, Mark Gerstein
& Michael Snyder
Nature Reviews Genetics 10,
57-63
Estimation of gene expression from RNA-seq: RPKM values
Number of reads which map per kilobase of exon per million
mapped reads for each gene
Theoretical Bioinfo
Dr. Benedikt Brors
Two samples from the same kidney carcinoma
Cancer – normal comparison
Cancer-normal comparison: significance?
MA-plot: Minus vs. Average
(Wikipedia)
Questions
• Differential genes between two conditions
(e.g., healthy/diseased)
• Coexpressed genes: pathways, coregulation
• Genes characteristic for particular
conditions (e.g., tumor staging)
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