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Why do we need good quality annotations?

Why do we need good quality annotations?. Pankaj Jaiswal Oregon State University Gene Annotation Workshop July 31, 2010 ASPB Plant Biology 2010 Montreal, Canada. Genotype. Polymorphism Candidate gene Gene models Transcripts Peptides Function Expression Pathway Homologs

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Why do we need good quality annotations?

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  1. Why do we need good quality annotations? PankajJaiswal Oregon State University Gene Annotation Workshop July 31, 2010 ASPB Plant Biology 2010 Montreal, Canada

  2. Genotype Polymorphism Candidate gene Gene models Transcripts Peptides Function Expression Pathway Homologs Paralogs Orthologs Interactions Genetic markers & phenotypes (genes and QTL) Map-1 Map-2 Physical and/or Sequence map Phenotype Comparative and Translational Genomics Forward Reverse

  3. Comparative Genomics Jaiswal lab: Strawberry Genome Consortium Schnable et al., pp. 1112 – 1115 (Maize synteny and Venn diagram)

  4. Expression pattern and over-represented metabolic processes of rice diurnally cycling genes 0 4 8 12 16 20 24 28 32 36 40 44 48 -500 0 500 Expression data provided by Todd Mockler, Analysis by Palitha Dharmawardhana (jaiswal lab)

  5. Trp pathway genes-Diurnal expression pattern clustering 0 4 8 12 16 20 24 28 32 36 40 44 48 Expression data provided by Todd Mockler, Analysis by Palitha Dharmawardhana (jaiswal lab)

  6. Diurnal variation of Trp biosynthetic gene expression 0 hrs 12 hrs 24 hrs 0 4 8 12 16 20 24 28 32 36 40 44 48 -200 0 200 Expression data provided by Todd Mockler, Analysis by Palitha Dharmawardhana (jaiswal lab)

  7. GO enrichment: Fruit GO enrichment: Root Over-represented gene ontology categories associated to genes expressed in (A) Fruit and (B) Root. The circles are shaded based on significance level (yellow = FDR below 0.05), and the radius of each circle denotes the number of genes in each category. Data provided by Todd Mockler and Kevin Folta

  8. Non plants Phenotype A B C D Maize, Rice and Others Arabidopsis and Others B2 A1 D KEGG-Rice Gene-Pathway Monocots Dicots A3 EC number Expression C Orthologs (Compara/Inparanoid) Text Mining A2 B1 B3 InterPro F Enriched Gene Function Function Gene Ontology MetaCyc Function Uniprot & RefSeq Manual Curation Pathways Interactions Genome/maps Genes

  9. Annotations by homology !

  10. Comparison of Metabolic Pathway Gene Annotations

  11. Race to the ……. ! Are we there yet ?

  12. Solutions ! • Get involved in the community curation • Provide details as much as possible in your publications • Work with your species specififc database (if available*) before/after publication on making sure data from your publication is integrated. • * If not available contact archives, succh as NCBI, Uniprot, Gramene. • You need it, I need it, community needs it.

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