GO tools available at AgBase

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GO tools availableat AgBase

• Fiona McCarthy, Shane Burgess, Susan Bridges
• The AgBase Databases, Institute of Digital
  Biology, Mississippi State University

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AgBase tools links.
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1. How much GO is available for my species?
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Taxon59729 Zebra finch
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2. Adding GO to your dataset.
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Example Netaffx
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2. Adding GO to your dataset.
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Text file of IDs - we want GO annotation. -
different database IDs How to get GO?
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1 Retrieve existing GO annotations.
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Select database.
many more (use All AgBase Databases
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Select accession type.
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Text file of IDs separated by a return.
Use Browse to select your input file
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GORetriever Results
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GORetriever Results
Save as an annotation file that represents your
dataset.
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GORetriever Results
GO Summary file can be saved as a text file and
used in GOSlimViewer to summarize function of
your dataset.
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GORetriever Results
List if IDs that have no GO annotation. Use
GOanna to add more GO.
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ADVANTAGES - quickly retrieves existing GO
data - reports on no matches DISADVANTAGES -
limited types of IDs accepted - can only find GO
annotation that is already in the
database GOanna - accepts fasta files
(resolves ID problems) - allows you to add GO
annotation
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GOanna
GOanna Blasts input sequences against a database
of GO annotated gene products.
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GORetriever Results
Prepare fasta files for these sequences Q5ZLE3,
NP_001019905, XP_416281 gt aa
sequences AI980246, BF845728 gt nt sequences
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GOanna Results
Save both unzipped files to the same directory or
folder.
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Query IDs in the Excel worksheet are hyperlinked
to BLAST data.
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Use link in the Excel document to view alignments
and decide what is a good match.
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If there is a good alignment to a protein with GO
? transfer GO to your record
If there is not a good alignment or the record
doesnt have GO ? literature
request annotation
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Excel file allows you to edit, delete, make your
own ga file.
good alignment
add to GO summary file (tab-delimited text file
containing ID, GOID, aspect)
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Contact AgBase to request GO annotation of
specific gene products.
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3. Summarizing function of your dataset
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GOSlimViewer summarizing results
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GOSlimViewer results
Detail file shows original GOID its slimmed
(or summarized) GOID.
View CC, MF, BP files shows summarized data for
each ontology.
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Copy paste file into text. Paste into Excel to
make graph.
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What can this information tell us?
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Looking at function, not genes Pie Graphs
relative proportions
apoptosis
immune response
cell-cell signaling
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GOModeler quantitative, hypothesis-driven
modeling. Coming soon (contact AgBase)
GOModeler
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McCarthy et al AgBase a functional genomics
resource for agriculture. BMC Genomics. 2006 Sep
87229.
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Gene Expression Analysis using GO
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http//www.geneontology.org/
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• However.
• many of these tools do not support farm animal
  species
• the tools have different computing requirements
• may be difficult to determine how up-to-date the
  GO annotations are
• Need to evaluate tools for your system.

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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?

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