` Comparison of Gene Ontology Term Annotations Between E.coli K12 Databases REDDYSAILAJA MARPURI WESTERN KENTUCKY UNIVERSITY

Why Genome Annotation? Annotation of a genome entails identification of genes in terms of precise start and end sites and description of cellular components, molecular functions and biological processes. Annotation forms the basis for extrapolation of gene functions based on similarity between protein sequences.

Gene Basic hereditary unit of a living organism Genome Entire complement of all genes Genome Annotation Process of attaching biological information to genome sequence Two main steps: 1) Gene Finding 2) Attaching biological information

Gene Sequence l DNA Gene Annotation By Ontology l Gene Ontology is described by a defined library of terms related to the cellular component, biological process and molecular functions of a gene in an organism. l

Increase in the wealth of the genomic data has led to the development of tools that assist in processing information about genes, their products and functions. Genome Ontology Important tool for annotation that uses Controlled vocabulary Hierarchy of terms

What is a cell ?

Why E.coli? E.coli K12 Primary Model Bacterial Organism Small genome size Much functional information Genome of E.coli K12 was sequenced in 1997.

The goal of this project was to compare automated annotation programs with validated hand curation.

Databases compared Ecocyc and BASys Ecocyc Most complete and standard Multi-dimensional annotation BASys Bacterial Annotation Systems Automated genome annotation system Built around 30 programs

Experimental Procedure Downloaded GO files and extracted non-redundant gene Id’s and GO terms using a program written in Mathematica.

4200 Genes estimated in E.coli of them have gene Id's and ontology's assigned by Ecocyc. Programs such as BASys that automatically annotate genes and assign Gene Ontology's have Id's and ontology's assigned by BASys. RESULTS

How many genes with Ontology from BASys were validated in Ecocyc? 253 genes in both Ecocyc and BASys have common ontology's.

Total GO Numbers in BASys and Ecocyc (2.8%) common to both databases (59.6%) unique to BASys (26.7%) unique to Ecocyc (10.88%) of them were non-assigned and are true negatives.

Conclusions 14% of BASys ontology assignments were validated with Ecocyc. But it missed 70% of validated annotations. BASys has liberal assignments and Ecocyc has more conservative assignments Liberal assignments tell us the direction to approach validating bench work.

REFERENCES : 1. Multi-dimensional annotation Of Escherichia coli K-12 Genome. Nucleic Acids Research, October 2007, Vol.35, BASys: a web server for automated bacterial genome annotation Nucleic Acids Research, April 2005, Vol.33, W455-W The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Research, 2004, Vol. 32. D262-D Functional Annotation of Arabidopsis Genome Using Controlled Vocabularies. Plant Physiology, June 2004, Vol. 135,

Acknowledgements Dr. Claire Rinehart

Thank you