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Gene Expression Analysis

Konstantin Tretyakov (kt@ut.ee)

BIIT Research group (http://biit.cs.ut.ee)

Science

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Observation Analysis Generalization

Science

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Observation Analysis Generalization

Science

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Observation Analysis Generalization

Science

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Observation Analysis Generalization

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Observation Analysis Generalizatin

Why?

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Why?

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Contemporary Science

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Observation Analysis Generalization

Contemporary Science

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Contemporary Science

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Contemporary Science

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Contemporary Science

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Observation Analysis Generalization

Contemporary Science

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Observation Analysis Generalization

Contemporary Science

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Observation Analysis Generalization

Data mining,

Data analysis, Statistical analysis,

Pattern discovery, Statistical learning,

Machine learning, Predictive analytics,

Business intelligence, Data-driven statistics

Inductive reasoning, Pattern analysis,

Knowledge discovery from databases,

Analytical processing,

…

Contemporary Bioinformatics

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Observation Analysis Generalization

Bioinformatics

Nucleotide

sequences

Molecular

interactions

Gene expression

Heredity

Drug effects

…

Contemporary Bioinformatics

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Observation Analysis Generalization

Bioinformatics

Nucleotide

sequences

Molecular

interactions

Gene expression

Heredity

Drug effects

…

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Bioconductor

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Why measure gene expression?

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How to measure expression?

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DNA

RNA

Protein

How to measure expression?

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DNA

RNA

Protein

How to measure expression?

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DNA

RNA

Protein

How to measure expression?

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RNA

How to measure expression?

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RNA

Microarray

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RNA

cDNA

Microarray

Microarray technology

cDNA

Oligonucleotide

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cDNA: 2-dye chip

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Normalization of 2-dye chips

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log(R) + log(G)

Lo

g(R

/G)

Affymetrix GeneChip

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$100-850

Millions of probes per cell

500 000 cells per chip Each probe = 25 bp

Affymetrix GeneChip

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10-20 probes, each 25 basepairs long

Gene

+ as many “mismatch” probes

Affymetrix GeneChip

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Affymetrix GeneChip

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Affymetrix GeneChip

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Affymetrix GeneChip

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Affymetrix GeneChip

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10-20 probes, each 25 basepairs long

Gene

+ as many “mismatch” probes

Probe1 = 2.0 Probe1 = 1.0 Probe3 = 1.5 …

.DAT

Gene1 = -1 Gene2 = 0.2 Gene3 = 1.2 …

.CEL .CSV

Gene expression databases

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Gene Expression Omnibus: http://www.ncbi.nlm.nih.gov/geo/

ArrayExpress: http://www.ebi.ac.uk/arrayexpress/

ArrayExpress

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ArrayExpress

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AffyBatch

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Dirty data

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Dirty data

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Normalization

Do we trust the measured data?

What to do with PM/MM?

How to match Probeset to a Gene?

How to normalize multiple chips?

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Normalization

Do we trust the measured data?

What to do with PM/MM?

How to match Probeset to a Gene?

How to normalize multiple chips?

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Gene expression data

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Expression data

Experiments

Ge

ne

s G(i,j)

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Comprehensive Identification of Cell Cycle-regulated Genes of the

Yeast Saccharomyces cerevisiae by Microarray Hybridization. Paul Spellman, et al. (1998)

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