instituto de engenharia de sistemas e computadores investigação e desenvolvimento em lisboa...

30-07-09KDBIO Group1

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa

technologyfrom seed

A database made in Portugal for the A database made in Portugal for the analysis of transcription regulatory associations analysis of transcription regulatory associations

in in yeastyeast

Regulat

ors

Search

Yeast

AndConsen

sus

Tracking

Transcr

iptional



technologyfrom seed

Motivation

• For a given ORF/Gene, identify regulatory associations• Search for Transcription Factors (TFs) acting on that ORF/Gene

• Use SGD or RSAT to retrieve the promoter sequence• Use TRANSFAC or SCPD to get a list of TFs binding sites• Use RSAT to search TFs bind sites within the promoter region• Use PUBMED to search for bibliographic references

• TRY TO IDENTIFY REGULATORY ASSOCIATIONS ...



technologyfrom seed

Motivation

www.yeastract.com



technologyfrom seed

Concepts

• Gene Ontology•Process•Function•Component

• Gene

• Protein

• Consensus



technologyfrom seed

Conceptual Model



technologyfrom seed

Data Extraction

-function-depth

function

-process-depth

process

-component-depth

component

*

* *

*

*

*

-regulationmode-reference-evidencecode

regulation

-orfname-genename-genesequence-promotersequence-url-retrotransposon-alternativenames

orfgene

YEASTRACTYEASTRACT

txttxt

txt

-consensus-variant

consensus

RSA Tools

34400 RA from >1000bibliographic references



technologyfrom seed

Graphic depictions of Transcriptional Regulatory Networks



technologyfrom seed

Yeastract-Discoverer



technologyfrom seed

Motif finders output



technologyfrom seed

# Accesses to YEASTRACT28 Jul 2008 – 28 Jul 2009

• >80 different countries

• >300 different institutions

• >16 000 visits

• >160 000 pageviews



technologyfrom seed

Origin of YEASTRACT users Map overlay – city view



technologyfrom seed

Origin of YEASTRACT users Ranking of Countries – top 20

1. United States2. Portugal3. Germany4. Spain5. United Kingdom6. France7. China8. Japan9. Taiwan10. Mexico

11. India12. Switzerland13. Brazil14. Poland15. Canada16. Australia17. Italy18. Sweden19. Netherlands20. Israel



technologyfrom seed

An example of successful cooperation

instituto de engenharia de sistemas e computadores investigação e desenvolvimento em lisboa...

Documents