What the biostatistician needs to know about molecular biology
#5

Format of these lectures

Microarrays

Hierarchical clustering

CAST (Ben-Dor)

WHICH CLUSTERING METHOD IS "BEST"?

WHICH GENES ARE UP-REGULATED?

STEP-DOWN TESTS FOR SIGNIFICANCE

Slide 9

Slide 10

Substitutes for the t-test

What genes are useful for classification?

What classifiers to use?

1D clustering vs.
2D "clustering"

Nonnegative matrix factorization

Slide 16

PLAID (Lazzeroni, Owen)

PLAID (continued)

Coverage of genes and experiments by blocks

Slide 20

Validation of 2D clustering models

PROTEOMICS

Slide 23

Why proteomics  ¹ transcriptomics

2D gels for protein separation

Slide 26

Isoelectric focusing

Slide 28

Slide 29

Slide 30

Slide 31

Gel informatics

Slide 33

Mass spectroscopy

Tandem MS (MS/MS)

ICAT (isotope-coded affinity tages)

Slide 37

Slide 38

Slide 39

Slide 40

Slide 41

Advantages/disadvantages of ICAT

Protein-protein interactions

Slide 44

Proteomics--the grand challenges

Slide 46