Getting GO: how to get GO for functional modeling

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Getting GO how to get GO for functional modeling

• Iowa State Workshop
• 11 June 2009

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• GO for your species
• GOProfiler summarizing the available GO
• GO browsers
• QuickGO from EBI
• AmiGO from the GO Consortium
• gene association files
• getting GO for your dataset
• adding more GO
• requesting GO
• GO based tools for functional modeling

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1. GO for your species
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GOProfiler

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

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• 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.

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2. GO Browsers
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Use GO Browsers for

• searching for GO terms
• searching for gene product annotation
• filtering sets of annotations and downloading
  results
• creating/using GO slims

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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/go.cgi
  
• Can search by GO Term or by UniProt ID
• Does not include IEA annotations

More information about these tools is available
from the online workshop resources.
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3. gene association files
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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.
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(additional column added to this example)
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gene product information
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metadata when who
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function information
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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

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

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GORetriever Results
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GORetriever Results
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GORetriever Results
save as text file For GOSlimViewer
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GORetriever Results
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But what about IDs not supported by GORetriever?
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5. Adding GO to your dataset
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• 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

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GOanna
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GOanna Results
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query IDs are hyperlinked to BLAST data (files
must be in the same directory)
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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.
WHAT IS A GOOD ALIGNMENT?
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• GOanna2ga
• New 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.

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6. Requesting GO
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7. GO based tools for biological modeling
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GOSlimViewer summarizing results
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response to stimulus
amino acid and derivative metabolic process
transport
behavior
cell differentiation
metabolic process
regulation 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
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http//www.geneontology.org/
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• However.
• many of these tools do not support agricultural
  species
• the tools have different computing requirements
• Tools for GO analysis of gene expression/microarra
  y data
• A 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.

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Evaluating GO tools

• Some criteria for evaluating GO Tools
• Does it include my species of interest (or do I
  have to humanize my list)?
• What does it require to set up (computer
  usage/online)
• What was the source for the GO (primary or
  secondary) and when was it last updated?
• Does it report the GO evidence codes (and is IEA
  included)?
• Does it report which of my gene products has no
  GO?
• Does it report both over/under represented GO
  groups and how does it evaluate this?
• Does it allow me to add my own GO annotations?
• Does it represent my results in a way that
  facilitates discovery?