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C u e r n a v a c a RegulonDB: Curation, Literature Search, Notation and Evidences about Transcriptional Regulation and Transcription Unit Organization In E. Coli K-12 Curators Meeting Milwaukee Wisconsin, 27th-28th October 2003 Program of Computational Genomics, CIFN, UNAM, A. P. 565-A, Cuernavaca, Morelos 62100, México. Socorro Gama-Castro Martin Peralta-Gil C I F N Centro de Investigación sobre Fijación de Nitrógeno

C u e r n a v a c a RegulonDB Database about gene transcriptional regulation and transcription unit organization in E.coli.

C u e r n a v a c a Data in RegulonDB 1. Genes 2. Products 3. Promoters 4. Terminators 5. Transcription unit 6. Regulatory proteins 7. Effectors 8. Conformations 9. Sites 10. Regulatory Interaction 11. Conditions Gene A Gene B Gene C RNA Proteins Terminator Promoter Transcription Unit Heat shock Anaerobiosis **Predictions * * * * *

C u e r n a v a c a opposite direction-identification Corregulation Overlapping genes Computational prediction Terminators Mutational Analysis Transcription-end-Mapping Stem-loop structure-identification Conditions Gene-Expression-Analysis Protein Conformation Binding-Of-Protein-effector In vitro essays Gene-Expression-Analysis Similarity-To-Consensus to bind an effector Regulatory Interaction Mutational Analysis Binding-Of-Purified-Proteins Binding-Of-Cellular-Extracts Similarity-To-Consensus Gene-Expression-Analysis Computational prediction Promoter Transcription-Initiation-Mapping Binding-Of-RNA-Polymerase Mutational Analysis of promoter Positional-Identification Computational prediction Transcription Unit Transcript-Length-Determination Mutational Analysis Promoter/Terminator-Identification Promoter/ downstream gene in Evidences and methods S1 mapping Primer extension cover method wconsensus-Patser operon detection, like hood Footprinting Mobility shift assays

C u e r n a v a c a araB, araA, araD = araBAD rpsU, dnaG, rpoD = rpsU-dnaG-rpoD dnaA, dnaN, rec = dnaAN-rec LacI transcriptional repressor CRP transcriptional dual regulator CaiF transcriptional activator BolA transcriptional regulator Repressor Activator Dual Unknown Transcription units Transcriptional Regulators Promoters dnaAp rpsUp araB p rpsUp1, rpsUp2, rpsUp3 Notation

C u e r n a v a c a Objects Statistics

C u e r n a v a c a References

C u e r n a v a c a Curation process at RegulonDB PubMed Select articles that are not cited on RegulonDB Read and select abstracts with transcriptional information REGULONDB Enter data into database through annotation forms Read complete articles about conditions Read complete general articles Article database Selected abstracts Is this a general article? Keywords Search Found Articles Articles Classification

C u e r n a v a c a Annotation forms

C u e r n a v a c a Annotation forms

C u e r n a v a c a ● Weekly curation meeting ● Community feedback ● Validation of data in the annotation forms ● Consistency checking Quality Control

C u e r n a v a c a Validation in the annotation forms Gene Regulatory protein Transcription Unit Conformation Promoter Terminator Regulatory interaction Product Effector References Evidences

C u e r n a v a c a Consistency checking

C u e r n a v a c a Consistency checking Promoters Promoters downstream List of promoters that are not upstream from their transcribed genes. gene Regulatory interaction Activators sites with central positions below -20 List of regulatory interactions, which activate the transcription, that were found to have a central position below –20. gene Transcription units With holes List of transcription units with missing intermediate genes. Genome araB araA araD araB araD TU

C u e r n a v a c a

● To add more objects to RegulonDB up elements Attenuators ● 2005 RegulonDB will have current information Goals

C u e r n a v a c a Principal Investigator: Julio Collado-Vides Curators: Alberto Santos Agustino Martinez Martin Peralta Socorro Gama Castro Programmers: Cesar Bonavides Delfino Garcia Edgar Diaz Fabiola Sanchez Heladia Salgado Veronica Jimenez Collaborators: EcoCyc Swiss Prot OU microarray DB RegulonDB Team

C u e r n a v a c a

Problemas comunes

C u e r n a v a c a Key Words Escherichia coli Operon Transcription unit Promoter Terminator Regulon Regulatory protein

C u e r n a v a c a RegulonDB has been useful for analysis in: Comparative genomics. Microarray analysis Construction of other data bases Evolution Prediction analysis Regulatory Models (experimental and theoretical) 49 papers have cited RegulonDB. Uses of RegulonDB