Why do we need good quality annotations? Pankaj Jaiswal Oregon State University Gene Annotation Workshop July 31, 2010 ASPB Plant Biology 2010 Montreal,

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Presentation transcript:

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

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

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

Expression pattern and over-represented metabolic processes of rice diurnally cycling genes Expression data provided by Todd Mockler, Analysis by Palitha Dharmawardhana (jaiswal lab)

Trp pathway genes-Diurnal expression pattern clustering Expression data provided by Todd Mockler, Analysis by Palitha Dharmawardhana (jaiswal lab)

Diurnal variation of Trp biosynthetic gene expression hrs12 hrs24 hrs Expression data provided by Todd Mockler, Analysis by Palitha Dharmawardhana (jaiswal lab)

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. GO enrichment: RootGO enrichment: Fruit Data provided by Todd Mockler and Kevin Folta

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

Annotations by homology !

Comparison of Metabolic Pathway Gene Annotations

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

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.