Prioritization of Avian GO Annotation Structural Annotation Genome

  • Slides: 10
Download presentation
Prioritization of Avian GO Annotation

Prioritization of Avian GO Annotation

Structural Annotation Genome No. Entrez Genes Species Build 2 Human Mouse Rat 1 Chicken

Structural Annotation Genome No. Entrez Genes Species Build 2 Human Mouse Rat 1 Chicken 36. 3 37. 1 3. 4 2. 1 36, 437 64, 018 49, 516 19, 9793 No. Proteins % predicted (NRPD) proteins 415, 830 228, 696 108, 069 31, 8193 4. 91 9. 28 29. 99 46. 624 proteins/gene 11. 41 3. 57 2. 18 1. 595 NRPD: Non-redundant Protein Database 1. The rat genome was published only 8 months prior to the chicken genome, yet rat has 2 x as many genes in Entrez Gene and 3 x as many proteins. 2. 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. 3. Chicken genes and proteins are under-represented in public databases. 4. Of the chicken proteins available from NRPD, almost half are predicted based upon computational analysis. 5. On average chicken has only 1 protein per gene so very little is known about isoforms and alternate transcripts in the chicken gene products.

Phase 1: “Breadth” n 7, 478 Chicken entries in Uni. Prot. KB ¨ GOA

Phase 1: “Breadth” n 7, 478 Chicken entries in Uni. Prot. KB ¨ GOA provides IEA mapping for Uni. Prot. KB entries Initial strategy for Ag. Base biocurators was to add GO to chicken gene products that had none. n Since 46% of the chicken proteins in NRPD were predicted, they would have no GO n ¨ IEA, ISS, ISO….

Functional Annotation 100 80 % of gene products annotated no GO 60 computational GO

Functional Annotation 100 80 % of gene products annotated no GO 60 computational GO Ag. Base 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

Phase 2: “Depth”

Phase 2: “Depth”

What are the community needs?

What are the community needs?

GO Annotation of Arrays Del. Mar 14 K, FHCRC, Tgu array n 44 K

GO Annotation of Arrays Del. Mar 14 K, FHCRC, Tgu array n 44 K Agilent oligo array n AIIM array, Affymetrix n Should we be focusing on arrays? n What arrays should we do? n

GO Annotation Priorities? Provide “breadth” of coverage n Annotate products represented on arrays n

GO Annotation Priorities? Provide “breadth” of coverage n Annotate products represented on arrays n Reference Genome targets n Subject areas (immunity, nutrition/metabolism, development n Ad hoc as requested n

Genome Annotation Dr Hilal AY Genome annotation GenomeGenome Annotation Dr Hilal AY Genome annotation Genome
Avian leucosis AVIAN LEUCOSIS Avian leucosis is aAvian leucosis AVIAN LEUCOSIS Avian leucosis is a
Annotation Traditional genome annotation BLAST Similarities Traditional genomeAnnotation Traditional genome annotation BLAST Similarities Traditional genome
Genome Annotation Continued This weeks lab Genome annotationGenome Annotation Continued This weeks lab Genome annotation
Genome analysis and annotation Genome Annotation Which sequencesGenome analysis and annotation Genome Annotation Which sequences
Functional Annotation and Functional Enrichment Annotation Structural AnnotationFunctional Annotation and Functional Enrichment Annotation Structural Annotation
Genome Sequence Annotation Server Structural and functional annotationGenome Sequence Annotation Server Structural and functional annotation
Annotation 1 Annotation 1 n n Override AnnotationAnnotation 1 Annotation 1 n n Override Annotation
Annotation What is an annotation An annotation isAnnotation What is an annotation An annotation is