Predicting biological function at different spatial scales

CREATED: 200808140305 Speaker: Peer Bock

Discovery process: 1) parts lists, 2) connectivity, 3) functionality across space and time

Homology in Metazoan genomes

identifying orthologous groups, eggnog.embl.de categories of orthologs: 1:1, N:N, patchy, insect-specific, vertebrate-specific, homology protein domains as functional units, evolution of phosphotyrosine signaling machinery genomic context, conserved neighborhood correct orthology analysis is crucial!

Protein networks

STRING server from EMBL, determining groups of orthologous genes Probabilistic predictions, von Merin (Nucleic Acid Research) Improvements

• increased resolution
• include other chemicals such as lipids, metabolites, etc
• include spatial and temporal aspects Chemical-Protein interaction prediction for drug retargetting using shared side effects Networks in 3D (spatial), SCB Mycoplasma project Networks in 4D (space + time)

Entire habitats

Comparative metagenomics Function prediction, Harrington (PNAS, 2007) Small families are hard to predict 4 levels of scale: gene/orthologous groups, operon, KEGG, functional classes (GO) Tools: iTOL and iPath