Transcript Introducing expression profiles

Cellular Profiles
Exploring gene expression profile patterns
Pathways, Profiles and Predictions
Brad Windle
Associate Professor of Medicinal Chemistry
Ph. # 628-1956
email [email protected]
Profile
A set of data that reflects something of significance
Cellular Profile
A set of data that reflects something of biological significance
A cell profile- may relate to a property of the cell
A cellular component profile- may relate to a property of
the component
Profiles are sometimes referred to as Signatures or Fingerprints
Cellular Profiles
Gene/Protein
Sequence
Protein
Structure
Protein
Expression
Gene
Expression
SNPs
Protein
States
Structural
Genomic
Cell State
Drug
Response
Drug
Structure
Methylation
Misc
Data
Metabolitics
Disease
Cellular Profiles
Gene/Protein
Sequence
Protein
Structure
Drug
Structure
Protein
Expression
Gene
Expression
SNPs
Protein
States
Structural
Genomic
Drug
Response
Methylation
Misc
Data
Metabolitics
Gene Expression Profiling
cell or condition
of interest
control or reference cell
hybridize to microarray
Structural Genomic Profiling
Comparative Genomic Hybridization (CGH)
cell with deletions
hybridize to metaphase
chromosomes
normal cell
CGH-arrays
cell with deletions
normal cell
hybridize to
BAC arrays
Methylation Profiling
me
CG
GC
me
Isolate or enrich for methylated DNA
total genomic DNA
Profiling Transcription Factor-Interactive DNA
Immuno-precipitate w/
Ab to protein
Chromatin IP or ChIP
total genomic DNA
Combinatorial Elements Regulating Transcription
The ProfileData Sources
Gene expression
DNA microarrays, oligo or PCR, 20-30,000 genes
Structural genomics
DNA microarrays, BACs, ~one per 1Mb
Methylation
DNA microarrays, upstream sequences, CpG islands
SNPs
DNA microarray, oligos, millions of SNP sites
Protein expression
Ab microarray, 2D gels, chromatographics
Protein states
2D gels, <1000 proteins resolved
Drug response
brute force, 70,000 compounds screened
Metabolitics
chromatographics
DNA/protein sequence
Sequencing, <20 people sequenced, brute force
Drug structure
in silico
Protein structure
3D crystallography, NMR, brute force
Gene
Expression
Profile
cell lines
1 2 3 4 5 6 7 8 9
genes
1
histone modification
2
histone modification
3
protein synthesis
4
histone modification
Classifying a Gene/Protein’s Function or Pathway
http://www.geneontology.org/
Exploring Gene Expression Profile Patterns
We’ll start with exploring profiles for 6000 genes in the
NCI 60 cell lines using the application Treeview.