Download 07:04, 7 August 2010

Why do we need good
quality annotations?
Pankaj Jaiswal
Oregon State University
Gene Annotation Workshop
July 31, 2010
ASPB Plant Biology 2010
Montreal, Canada
Comparative and Translational Genomics
Forward
Genotype
Polymorphism
Candidate gene
Gene models
Transcripts
Genetic markers &
phenotypes (genes
and QTL)
Peptides
Function
Expression
Pathway
Homologs
Map-1
Map-2
Reverse
Phenotype
Physical and/or
Sequence map
Paralogs
Orthologs
Interactions
2
Comparative Genomics
Schnable et al., pp. 1112 – 1115 (Maize synteny and Venn diagram)
Jaiswal lab: Strawberry Genome Consortium
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 hrs
12 hrs
24 hrs
0
-200
4
8 12 16 20 24 28 32 36 40 44 48
0
200
Expression data provided by Todd Mockler, Analysis by Palitha Dharmawardhana (jaiswal lab)
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
Non plants
Maize, Rice and Others
Phenotype
Arabidopsis and Others
KEGG-Rice Gene-Pathway
EC number
Expression
Text
Orthologs (Compara/Inparanoid)
Mining
InterPro
Monocots
Dicots
Enriched
Gene
Function
Genes
A
B
C
Uniprot
&
RefSeq
D
B2
A1
MetaCyc
Function
Function
Gene Ontology
Manual
Curation
D
A3
Pathways
C
A2
B1
F
Interactions
B3
Genome/maps
8
Annotations by homology !
Comparison of Metabolic Pathway Gene Annotations
Race to the ……. !
Are we there yet ?
11
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.