Prioritization of Avian GO Annotation

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Prioritization of Avian GO Annotation
2
Structural Annotation
predicted proteins
No. Proteins (NRPD)
Genome Build2
No. Entrez Genes
Species
proteins/gene
11.41
4.91
415,830
36,437
36.3
Human
3.57
9.28
228,696
64,018
37.1
Mouse
2.18
29.99
108,069
49,516
3.4
Rat1
1.595
46.624
31,8193
19,9793
2.1
Chicken
NRPD Non-redundant Protein Database

• The rat genome was published only 8 months prior
  to the chicken genome, yet rat has 2x as many
  genes in Entrez Gene and 3x as many proteins.
• After two genome builds chicken still has 5 of
  genomic sequence that has not been assigned a
  chromosome and mini-chromosomes have not been
  sequenced.
• Chicken genes and proteins are under-represented
  in public databases.
• Of the chicken proteins available from NRPD,
  almost half are predicted based upon
  computational analysis.
• On average chicken has only 1 protein per gene
  so very little is known about isoforms and
  alternate transcripts in the chicken gene
  products.

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Phase 1 Breadth

• 7, 478 Chicken entries in UniProtKB
• GOA provides IEA mapping for UniProtKB entries
• Initial strategy for AgBase biocurators was to
  add GO to chicken gene products that had none.
• Since 46 of the chicken proteins in NRPD were
  predicted, they would have no GO
• IEA, ISS, ISO.

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Functional Annotation
100
80
no GO
60
of gene products annotated
computational GO
AgBase
40
manual GO
20
0
Human
Mouse
Rat
Chicken
the proportion of GO for chicken is
over-represented because of their
under-representation in public databases
6
Phase 2 Depth
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What are the community needs?
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GO Annotation of Arrays

• DelMar14K, FHCRC, Tgu array
• 44K Agilent oligo array
• AIIM array, Affymetrix
• Should we be focusing on arrays?
• What arrays should we do?

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GO Annotation Priorities?

• Provide breadth of coverage
• Annotate products represented on arrays
• Reference Genome targets
• Subject areas (immunity, nutrition/metabolism,
  development
• Ad hoc as requested