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C I F N Centro de Investigación sobre Fijación de Nitrógeno. RegulonDB: Curation, Literature Search, Notation and Evidences about Transcriptional Regulation and Transcription Unit Organization In E. Coli K-12. C u e r n a v a c a.

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

  2. Database about gene transcriptional regulation and transcription unit organization in E.coli. http://www.cifn.unam.mx/Computational_Genomics/regulondb RegulonDB

  3. Transcription Unit Promoter Terminator Gene C Gene A -10 Gene B -35 RNA Proteins * * * **Predictions * * Heat shock Anaerobiosis 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

  4. 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 Footprinting 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 Mobility shift assays operon detection, like hood wconsensus-Patser S1 mapping Primer extension cover method Evidences and methods

  5. Transcription units rpsU, dnaG, rpoD = rpsU-dnaG-rpoD araB, araA, araD = araBAD dnaA, dnaN, rec = dnaAN-rec Promoters rpsUp rpsUp1, rpsUp2, rpsUp3 dnaAp araBp Transcriptional Regulators LacI transcriptional repressor Repressor CaiF transcriptional activator Activator CRP transcriptional dual regulator Dual BolA transcriptional regulator Unknown Notation

  6. Objects Statistics

  7. 1997 1998 1999 2000 2001 2002 2003 References

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

  9. Annotation forms

  10. Annotation forms

  11. Quality Control • Weekly curation meeting • Community feedback • Validation of data in the annotation forms • Consistency checking

  12. Product Regulatory protein Promoter Gene Terminator Effector References Conformation Evidences Transcription Unit Regulatory interaction Validation in the annotation forms

  13. Consistency checking

  14. Promoters gene Promoters downstream List of promoters that are not upstream from their transcribed genes. gene Regulatory interaction -35 -10 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. Transcription units With holes List of transcription units with missing intermediate genes. araB araA araD Genome araB araD TU Consistency checking

  15. Goals • To add more objects to RegulonDB up elements Attenuators • 2005 RegulonDB will have current information

  16. RegulonDB Team 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

  17. Problemas comunes

  18. Escherichia coli • Operon • Transcription unit • Promoter • Terminator • Regulon • Regulatory protein Key Words

  19. Uses of RegulonDB 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.

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