Why do we need good quality annotations
This presentation is the property of its rightful owner.
Sponsored Links
1 / 12

Why do we need good quality annotations? PowerPoint PPT Presentation


  • 45 Views
  • Uploaded on
  • Presentation posted in: General

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

Download Presentation

Why do we need good quality annotations?

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Why do we need good quality annotations

Why do we need good quality annotations?

PankajJaiswal

Oregon State University

Gene Annotation Workshop

July 31, 2010

ASPB Plant Biology 2010

Montreal, Canada


Why do we need good quality annotations

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


Why do we need good quality annotations

Comparative Genomics

Jaiswal lab: Strawberry Genome Consortium

Schnable et al., pp. 1112 – 1115 (Maize synteny and Venn diagram)


Expression pattern and over represented metabolic processes of rice diurnally cycling genes

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

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

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)


Go enrichment root

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


Why do we need good quality annotations

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


Annotations by homology

Annotations by homology !


Why do we need good quality annotations

Comparison of Metabolic Pathway Gene Annotations


Why do we need good quality annotations

Race to the ……. !

Are we there yet ?


Solutions

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.


  • Login