1. Advanced PGDB Editing: Gene Ontology (GO) Terms
Ingrid M. Keseler
Bioinformatics Research Group
SRI International
Presented by Peter E. Midford

2. Gene Ontology (GO) Terms

3. Motivation: Why GO Terms?
For example:
Standardization of annotation helps others
Data mining across genomes
Genome annotation by similarity (e.g. via InterPro, Pfam, TIGRFAM, COG mappings)
It helps you:
Omics data clustering
Cross-checking with different annotation source

4. A Word (Or Two) About GO Learn what you can about using GO
Surf the geneontology.org web site
Attend a GO Annotation Camp
Ask questions on the GO mailing lists
Request new GO terms if appropriate
Useful for everybody
Have input when it counts
A new GO database can be incorporated into Pathway Tools; request help with setting up the process
Computational GO term assignments may be available for your genome via UniProt

5. GO Classification Editor
Accessible via the Protein Editor
Expand/contract, select/deselect by clicking on +/- and the actual terms
Selected items move to “Selections” section
Search feature: can search by name/substring or GO id (in the full format only, e.g. “GO: ”, not just the number)
For example, search for “arginine” yields many options
Click an option to highlight in hierarchy
Hovering over a term in the hierarchy brings up its definition in the middle panel
Must still click on entry in hierarchy to select the term for annotating the protein

6. Caveats Implementation of GO in Pathway Tools is incomplete, e.g.
Only one qualifier, “with”, is implemented
No annotation extensions
If you are interested in a more complete implementation of the GO ontology and curation capabilities, please let us know

7. Importing GO Terms via UniProt IDs (1)
Download annotation file from geneontology.org:
You probably want the UniProt [multispecies] file
Use the ftp: address and either an ftp app (e.g., FileZilla, CyberDuck) or the command line curl tool to download the uniport file
e.g., curl ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniport_all.gaf.gz > goa_uniport_all.gaf.gz

8. Importing Go Terms via UniProt IDs (2)
Unzip the file and use grep, or use zgrep directly, to extract annotations for your organism by taxID
zgrep ‘taxon:85962’ goa_uniport_all.gaf.gz > goa_uniport_85962
Beware that these are large files and may take a long time to download (e.g. 7 hrs), a long time to unzip, and a long time to grep through (i.e. don’t try this here)

9. Importing GO Terms
May at some point be made into a GUI tool within Pathway Tools; at this time, it is a command line operation
At the lisp prompt, with your database opened:
(update-uniprot-go-annots ”filepath”)
Where filepath is replaced with e.g.
/Users/midford/Documents/demo/goa_uniport_85962
Some log files are written into the same directory; do some sanity checking of the files and the database before saving
Import citations

10. Advanced PGDB Editing: Regulation
Ingrid M. Keseler
Bioinformatics Research Group
SRI International
Presented by Peter E. Midford

11. Motivation: Why Regulation?
For example:
Genome and regulatory overview
Global perspective
Omics data
Data sets for promoter prediction etc.

12. Omics Viewer: Regulatory Overview
Data from J Bacteriol Feb;192(3): A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation.

13. Defining a New Transcription Unit
Gene > New Operon
Key elements – gene names in order
PTools will prompt you for a citation for the TU
Specify promoter
Can use absolute or relative position of transcription start site
PTools will calculate the other value for you
PTools will prompt you for a citation for the TSS
Specify sigma factor (if appropriate)
It may be necessary to first classify sigma factors under |Sigma-Factors|

14. Adding Transcription Factor Binding Sites
Click on TU name – Edit > Create Regulatory Interaction
Select type of regulatory interaction
Can put in a protein name, or select a defined TF
Indicate whether it activates, represses or both
Define relative distance from transcription start site
Draws DNA footprint from feature defined in TF
Can edit TF binding sites by clicking on site name
Edit > Regulatory Interaction Editor
Can add summaries and citations
This builds the transcriptional regulatory network

15. More Regulatory Interactions
Attenuation
Regulation of translation
RNA-mediated
Protein-mediated
Small molecule-mediated
Regulated protein or mRNA degradation (planned)
If you have suggestions for types of regulation you would like to represent, or for improvements on what is there, please let us know.
Tools for genome-scale datasets?