Why do we need good quality annotations?

Pankaj JaiswalOregon State University

Gene Annotation WorkshopJuly 31, 2010

ASPB Plant Biology 2010Montreal, 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 ConsortiumSchnable et al., pp. 1112 – 1115 (Maize synteny and Venn diagram)

Comparative Genomics

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)

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)

Diurnal variation of Trp biosynthetic gene expression

0 4 8 12 16 20 24 28 32 36 40 44 48

0 hrs 12 hrs 24 hrs

-200 0 200

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

FunctionGene Ontology

Genes

EC numberText Mining

Phenotype

KEGG-Rice Gene-Pathway

Expression

Manual Curation

InteractionsPathways

Enriched Gene

Function

Monocots Dicots

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.