1. Advanced PGDB Editing: Regulation GO Terms
Ingrid M. Keseler
Bioinformatics Research Group
SRI International

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

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

4. 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|

5. 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

6. 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?

7. Gene Ontology (GO) Terms

8. Motivation: Why GO Terms?
For example:
Standardization of annotation
Data mining across genomes
Genome annotation by similarity (e.g. via InterPro, Pfam, TIGRFAM, COG mappings)
Microarray data clustering
Etc.

9. 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

10. 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