Getting GO: how to get GO for functional modeling

Iowa State Workshop11 June 2009

1. GO for your species GOProfiler: summarizing the available GO

2. GO browsers QuickGO from EBI AmiGO from the GO Consortium

3. gene association files4. getting GO for your dataset5. adding more GO6. requesting GO7. GO based tools for functional modeling

1. GO for your species

GOProfiler

GOProfiler allows you get an overview of what GO annotation exists for the species you are interested in.

Number of proteins is based upon UniProtKB records for these species.

Species with only IEA annotations do not have an active GO annotation project GO provided automatically by EBI GOA

Project.

2. GO Browsers

Use GO Browsers for:

searching for GO terms searching for gene product annotation filtering sets of annotations and

downloading results creating/using GO slims

GO Browsers QuickGO Browser (EBI GOA Project)

http://www.ebi.ac.uk/ego/Can search by GO Term or by UniProt ID Includes IEA annotations

AmiGO Browser (GO Consortium Project)http://amigo.geneontology.org/cgi-bin/amigo/g

o.cgiCan search by GO Term or by UniProt IDDoes not include IEA annotations

More information about these tools is available from the online workshop resources.

3. gene association files

The gene association (ga) file standard file format used to capture GO annotation

data tab-delimited file containing 15* fields of information:

Information about the gene product (database, accession, name, symbol, synonyms, species)

information about the function: GO ID, ontology, reference, evidence, qualifiers, context

(with/from) data about the functional annotation

date, annotator* 2 additional fields will soon be added to capture information about isoforms and other ontologies.

(additional column added to this example)

gene product information

metadata: when & who

function information

Gene association files GO Consortium ga files

many organism specific files also includes EBI GOA files

EBI GOA ga files UniProt file contains GO annotation for all species

represented in UniProtKB AgBase ga files

organism specific files AgBase GOC file – submitted to GO Consortium & EBI

GOA AgBase Community file – GO annotations not yet

submitted or not supported all files are quality checked

4. Finding GO for your dataset

The AgBase GO annotation tools can be used separately or can be combined to rapidly provide an annotation file for functional modeling tools.

GORetriever Allows you to get GO annotations for a specific set

of gene products. Accepts a text file of UniProt accessions or IDs or

gi numbers. Returns GO annotations, list of accessions that had

no GO and a GO Summary file.

GORetriever Results

GORetriever Results

GORetriever Results

save as text fileFor GOSlimViewer

GORetriever Results

But what about IDs not supported by GORetriever?

5. Adding GO to your dataset

only returns existing GO only accepts limited accession types

GOanna does a Blast search against existing GO annotated products.

allows you to quickly transfer GO to gene products where they have similar sequences (ISS)

accepts fasta files

GOanna

GOanna Results

query IDs are hyperlinked to BLAST data(files must be in the same directory)

*WHAT IS A GOOD ALIGNMENT?

1. Manually inspect alignments and delete any lines where there is not a good alignment*.2. Add this additional annotation to the annotations from GORetriever.

GOanna2gaNew to AgBase: an online script to convert your GOanna file to a gene association file format.

• Allows you to add manually checked GOanna annotations to a GORetriever file.• Link is available from the workshop resources.

6. Requesting GO

7. GO based tools for biological modeling

GOSlimViewer: summarizing results

response to stimulus

amino acid and derivative metabolic processtransportbehavior

cell differentiation

metabolic processregulation of biological process

cell communication

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

cell death

cell motility

macromolecule metabolic process

multicellular organismal development

catabolic process

biological_process

“process unknown”“function unknown”“component unknown”

??

http://www.geneontology.org/

However…. many of these tools do not support agricultural

species the tools have different computing requirements Tools for GO analysis of gene

expression/microarray dataA list of these tools that can be used for

agricultural species is available on the workshop website at the Expression analysis tools at the GO consortium website link.

Evaluating GO toolsSome criteria for evaluating GO Tools:1. Does it include my species of interest (or do I have to

“humanize” my list)?2. What does it require to set up (computer usage/online)3. What was the source for the GO (primary or secondary) and

when was it last updated?4. Does it report the GO evidence codes (and is IEA included)?5. Does it report which of my gene products has no GO?6. Does it report both over/under represented GO groups and

how does it evaluate this?7. Does it allow me to add my own GO annotations?8. Does it represent my results in a way that facilitates

discovery?