Comparative Genomics: Surveys of a Finite Parts List
PPT Slide
World of Structures is even more Finite, providing a valuable simplification
A Parts List Approach to Bike Maintenance
A Parts List Approach to Bike Maintenance
Comparing Genomes in terms of Protein Structure: Surveys of a Finite Parts List
Fold Library vs. Other Fundamental Data structures
Fold Library: scop + Automatic Alignments
Some Similarities are Readily Apparent others are more Subtle
Some Similarities are Readily Apparent others are more Subtle
P-values
EVD Fits
Same EVD Results for Sequence & Struct.
Chothia & Lesk, 1986 revisited, 32 ?16K pts.
Chothia & Lesk, 1986 revisited, 32 ?16K pts.
Problems with RMS and %ID
Modern statistical language
Comparing Genomes in terms of Protein Structure: Surveys of a Finite Parts List
At What Structural Resolution Are Organisms Different?
Practical Relevance of Structural Genomics
Cross-Reference: Folds?Sequences ? Organisms
Shared Folds
Cluster Trees Grouping Initial Genomes on Basis of Shared Folds
Distribution of Folds in Various Classes
Common Folds in Genome, Varies Betw. Genomes
Characteristics of Common, Shared Folds: bab structure
Bias Problem ? Prediction, Expts.
Finding Unusual Proteins for Expt. Structural Genomics
Characterizing the Low-hanging Fruit for Experimental Structural Genomics
TM-helix “prediction”
2º Structure Prediction
Different Amino Acid Composition Should Give Different 2º Structure
Comparing Genomes in terms of Protein Structure: Surveys of a Finite Parts List
Adding Structure to Functional Genomics, Function to Structural Genomics
Functional Classification
A Simple Scheme for Functionally Classifying Protein Structures
Fold-Function Combinations
Relationship of Similarity in Sequence & Structure to that in Function
Relationship of Similarity in Sequence & Structure to that in Function II
Fold-Function Combinations #2
Fold-Function Combinations
Most Versatile Folds & Functions
Fold-Function Combinations Cross-Tabulation Summary Diagram
Compare Classifications and Genomes
Different Structure Function Relationships for Most Ancient Proteins
Comparing Genomes in terms of Protein Structure: Surveys of a Finite Parts List
Gene Expression Datasets: the Transcriptome
Composition of Genome vs. Transcriptome
Relation between Length & Expression
Composition of Transcriptome in terms of Broad Structural Classes
Which Protein Folds are Highly Expressed?
Composition of Transcriptome in terms of Functional Classes
Expression Level is Related to Localization
Bayesian System for Localizing Proteins
Bayesian System for Localizing Proteins
Results on Testing Data
Results on Testing Data #2
Extrapolation to Compartment Populations of Whole Yeast Genome: ~4000 predicted + ~2000 known
Cluster Expression Data, Relate to MIPS Functional Category
Correlation of Functional Class and Expression – not that strong
Whole Genome Phenotype Profiles
Phenotype ORF Clustering
GeneCensus
Comparing Genomes in terms of Protein Structure: Surveys of a Finite Parts List
Macromolecular Motions
Motions DB: Information, Size, then Packing Based Classification
Interface Packing and Motions
Packing Based Classification: Hinge v Shear
Proteins With Shear Motions are Often Divided into Layers
Packing Based Classification: Hinge v Shear
Voronoi Volumes, the Natural Way to Measure Packing
ProtOr Parameter Set: Standard Radii & Volumes
Motion Analysis Server, Morph Movies
5 Movies Generated by the Server
Comparing Genomes in terms of Protein Structure: Surveys of a Finite Parts List