Ciência 2010, Lisboa – The YEASTRACT database: 4 years of success in deciphering transcription regulation in yeast at a genome-wide level IBB – Institute for Biotechnology and Bioengineering, Centro de Engenharia Biológica e Química, IST Miguel Cacho Teixeira

Ciência 2010, Lisboa – Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Freitas AT, Oliveira AL, Sá-Correia I, 2006, Nucleic Acids Res. Database Issue. 34: D446-D451.

Ciência 2010, Lisboa – International impact of YEASTRACT > 1600 institutions > 70 countries > 500,000 queries since 2006 > 100 citations of our 1 st paper Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Freitas AT, Oliveira AL, Sá-Correia I, 2006, Nucleic Acids Res. Database Issue. 34: D446-D451. Monteiro P, Mendes N, Teixeira MC, d'Orey S, Tenreiro S, Mira NP, Pais H, Francisco A, Carvalho A, Lourenço AB, Sá-Correia I, Oliveira AL, Freitas AT, 2008, Nucleic Acids Res. Database Issue 36: D132-D136. Abdulrehman D, Monteiro PT, Teixeira MC, Mira NP, Lourenço AB, dos Santos SC, Cabrito TR, Francisco AP, Madeira SC, Aires RS, Oliveira AL, Sá-Correia I, Freitas AT, submitted.

Ciência 2010, Lisboa – Transcriptional regulation in yeast

Ciência 2010, Lisboa – YEASTRACT database conceptual model consensusdata -reference consensus -consensus -variant protein -proteinname -aminoacidsequence -description function -function -depth component -component -depth process -process -depth potentialregulation -frwstrandpos -frwstrandlen -revstrandpos -revstrandlen regulation -reference Translation orfgene -orfname -genename -genesequence -promotersequence -url -alternativenames Potential regulation – a putative transcription factor binding site occurs in the promoter region of the potential target-gene Documented regulation – there is published experimental evidence that proves that the trasncription factor binds to the promoter region of its target genes (considered direct evidence) or that it affects the expression of its target genes (considered indirect evidence)

Ciência 2010, Lisboa – YEASTRACT txt RSA Tools >6000 gene promoter sequences >6000 gene descriptions and associated GO term >48000 documented regulatory associations, collected from over 1200 references 298 DNA binding sites 149 transcription factors Data collection

Ciência 2010, Lisboa – Example 1 Identify the potential or documented regulators of a given gene Potential regulators of FLR1 or TPO1 genes TRANSCRIPTION REGULATORY NETWORK FOR A SINGLE GENE, FLR1 Teixeira MC, Dias PJ, Simões T, Sá-Correia I, 2008, Biochem Biophys Res Commun, 367, Teixeira MC, Dias PJ, Monteiro PT, Oliveira AL, Freitas AT, Sá-Correia I, submitted Monteiro PT, Dias PJ, Ropers D, Oliveira AL, Sá-Correia I, Teixeira MC, Freitas AT, submitted.

Ciência 2010, Lisboa – Example 2 Grouping a list of genes based on shared regulatory associations with transcription factors (transcriptomics/proteomics data analysis) Santos PM, Simões T, Sá-Correia I, 2009, Proteomics, 19,

Ciência 2010, Lisboa – Example 3 Identify new DNA motifs and compare them to transcription factor binding sites DNA motif found to be over-represented in the promoter regions of the Pdr1p target-genes

Ciência 2010, Lisboa – Acknowledgements FEDER, FCT (projects POCTI/BIO/38115/2001, POSI/SRI/47778/2002, POSI/EIA/57398/2004, POCTI/BIO/56838/2004 and PTDC/EIA/67722/2006 and PhD and post-doctoral grants) Current contributors Past contributors Miguel Teixeira Isabel Sá-CorreiaNuno Mira Tânia Cabrito Artur LourençoSandra dos Santos Pedro Monteiro Ana T FreitasArlindo OIiveira Dário Abdulrehman Sara Madeira Alexandre Francisco 1 st release: The Yeastract database: Pooja Jain, Sandra Tenreiro, Alexandra Fernandes, Marta Alenquer 2 nd release: Yeastract-discoverer: Nuno Mendes, Sofia D’Orey, Sandra Tenreiro, Hélio Pais, Alexandra Carvalho 3 rd release: Yeastract web services Joana Gonçalves Ricardo Aires