why do we need good quality annotations? pankaj jaiswal oregon state university gene annotation...
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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
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.