cellular profiles exploring gene expression profile patterns pathways, profiles and predictions brad...
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Cellular Profiles
Exploring gene expression profile patterns
Pathways, Profiles and Predictions
Brad WindleAssociate Professor of Medicinal ChemistryPh. # 628-1956email [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
GeneExpression
ProteinExpression
MiscData
SNPs
Methylation
Cell State
Drug Response
Metabolitics
StructuralGenomic
ProteinStates
Disease
Gene/ProteinSequence
ProteinStructure
DrugStructure
Cellular Profiles
GeneExpression
ProteinExpression
MiscData
SNPs
MethylationDrug
Response
Metabolitics
StructuralGenomic
ProteinStates
Gene/ProteinSequence
ProteinStructure
DrugStructure
cell or conditionof interest
control or reference cell
hybridize to microarray
Gene Expression Profiling
Comparative Genomic Hybridization (CGH)
Structural Genomic Profiling
cell with deletions normal cell
hybridize to metaphase chromosomes
CGH-arrays
cell with deletions normal cell
hybridize toBAC arrays
Methylation Profiling
me
me
CGGC 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
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 DNA microarrays, oligo or PCR, 20-30,000 genes
Structural genomics DNA microarrays, BACs, ~one per 1Mb
Methylation DNA microarrays, upstream sequences, CpG islands
Gene Expression
Profile
cell lines
genes1
2
3
4
1 2 3 4 5 6 7 8 9
histone modification
histone modification
histone modification
protein synthesis
http://www.geneontology.org/
Classifying a Gene/Protein’s Function or Pathway
Exploring Gene Expression Profile Patterns
We’ll start with exploring profiles for 6000 genes in theNCI 60 cell lines using the application Treeview.